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[Clarity-cvs] Is Israel a Democracy? -- The problem with intellectually insecure whites -- Should Christians Support Israeli Terrorism in Gaza?
by Lawrence Auster 23 Jan '09

23 Jan '09

The Jewish State of Israel has no constitution, nor does it name its borders. Israel's hidden constitution is Judaism. Israel's undeclared borders range from the Nile to the Euphrates rivers. Israel's desired jurisdiction extends over the entire Earth. It could not be more clear that the Jewish State follows a foreign policy which obeys Jewish Law as iterated in the Hebrew Bible, the Talmud, Maimonedes, the Cabalah, and the many commentaries and refinements of same. The Jews are genociding the native inhabitants of Palestine, just as their religion advises, and because their religion teaches them to do so. They treat non-Jews as if non-humans, just as their religion requires them to do. They make perpetual war on every nation on Earth, just as their genocidal Jewish God has instructed. The Jews of Israel are simply being Jews. Jews are an existential threat to the human race. Israel contains one third of the Jews of the World. It is not some aberration of the Jewish spirit, but the condensation and concentration of the perverse Jewish mentality, which malady also pervades the remaining two thirds of Jewry, who almost unanimously support the Jewish State, and who certainly do unanimously support the Jewish People and its consistent and constant crimes against the human race. Israel is Jewry and the danger of Israel is the danger of the Jewish People to all others, as the Jews have demonstrated each and every day of their existence. The Jews, the entire Jewish People of 15 million, will not relent until they have wiped out all non-Jews in "Greater Israel". They will not stop destroying all other cultures, nations, religions, ethnicities, races, competition, etc. until they are either stopped, or succeed in their ancient quest to destroy the human race. What Israel is doing is not some reaction to outside forces, nor was the formation of Israel a response to the Holocaust. Israel is simply following the plan laid out in the Jews' religious texts. The Jews have openly planned to take Palestine and genocide the native population of Palestine for some 2,500 years before the Holocaust. The Jews have openly complained that "anti-Semitism" is a threat that gives them the right to genocide the Palestinians, not merely since the advent of Nazism, but for some 2,500 years. The Jewish religion is the Constitution of the Jewish State of Israel, and, to a greater or lesser extent, the constitution of the nature of every Jew alive. The borders of Israel are the range the Jew roams over the entire World. The perverse Jewish mentality is inbred by a Jew's exposure to his parents and to his community. Judaism passes in the spit and slobber of Jewish mother telling her Jewish child that he is a "Jew", as much as Judaism passes in the poison and pain of a Talmudic tractate. The secular Jews did not suddenly come to life after the Enlightenment and the Jewish Reformation a body of vampires that appeared ex nihilo, in vacuo, mostly atheistical and undetached from formally practiced Judaism. Judaism is the Jew. It is a mindset that transcends and supercedes religion. It is a belief set, a way of life, a perception of one's self and one's relation to the World that makes a Jew, a Jew, and a danger to all of humanity. In fact, the religious shell of Judaism is like the stretched and infected skin of a lycanthropic pustule. When you lance it to cure the infection, the virus only becomes more contagious and spills directly on the non-Jew. The secular Jew is a deliberate product of the hyper-religious Jew, a monster created out of the hewed corpses of the fanatically religious Jew, a Golem which is conjured up to enter the World of the non-Jew and poison its blood, and boil its brain with a rabid lunacy that bites and spreads, until the infected community feeds on itself and fills the fields with rotting bloating bodies, where once human beings tilled the soil and tended to their families. The religious Jew created the secular Jew as an army of Esthers who seduce with open thighs, broad smiles, and a Siren call that lures in the non-Jew to cast his skull upon the jagged rocks and color the seas with his blood, sickened and blinded by the venereal disease of Judaism in secular form. Israel is not a secular democracy. It is a religious mockery. It is a rabid bat flying to the ends of the Earth, to end the Earth. No one will be free nor safe until the disease is quarantined and dies out. Source: http://www.ziopedia.org/articles/israel/how_can_israel_claim_to_be_a_%27dem… -------------------- The problem with intellectually insecure whites By Kevin MacDonald January 19, 2009 America will soon have a white minority. This is a much desired state of affairs for the hostile elites who hold political power and shape public opinion. But it certainly creates some management issues � at least in the long run. After all, it�s difficult to come up with an historical example of a nation with a solid ethnic majority (90% white in 1950) that has voluntarily decided to cede political and cultural power. Such transformations are typically accomplished by military invasions, great battles, and untold suffering. And it�s not as if everyone is doing it. Only Western nations view their own demographic and cultural eclipse as a moral imperative. Indeed, as I have noted previously, it is striking that racial nationalism has triumphed in Israel at the same time that the Jewish intellectual and political movements and the organized Jewish community have been the most active and effective force for a non-white America. Indeed, a poll in 2008 found that Avigdor Lieberman was the second most popular politician in Israel. Lieberman has advocated expulsion of Arabs from Israel and has declared himself a follower of Vladimir Jabotinsky, the leading pioneer of racial Zionism. The most popular politician in the poll was Benjamin Netanyahu � another admirer of Jabotinsky. Prime Minister Ehud Olmert and Foreign Minister Tzipi Livni are also Jabotinskyists. The racial Zionists are now carrying out yet another orgy of mass murder after a starvation-inducing blockade and the usual triggering assault designed to provoke Palestinian retaliation � which then becomes the cover for claims that Israel is merely defending itself against terrorism. This monstrosity was approved by overwhelming majorities of both Houses of Congress. The craven Bush administration did its part by abstaining from a UN resolution designed by the US Secretary of State as a result of a personal appeal by the Israeli Prime Minister. This is yet another accomplishment of the Israel Lobby, but one they would rather not have discussed in public. People might get the impression that the Lobby really does dictate US foreign policy in the Mideast. Obviously, such thoughts are only entertained by anti-Semites. But I digress. In managing the eclipse of white America, one strategy of the mainstream media is to simply ignore the issue. Christopher Donovan (�For the media, the less whites think about their coming minority status, the better�) has noted that the media, and in particular, the New York Times, are quite uninterested in doing stories that discuss what white people think about this state of affairs. It�s not surprising that the New York Times � the Jewish-owned flagship of anti-white, pro-multicultural media � ignores the issue. The issue is also missing from so-called conservative media even though one would think that conservatives would find the eclipse of white America to be an important issue. Certainly, their audiences would find it interesting. Now we have an article �The End of White America� written by Hua Hsu, an Assistant Professor of English at Vassar College. The article is a rather depressing display of what passes for intellectual discourse on the most important question confronting white people in America. Hsu begins by quoting a passage in F. Scott Fitzgerald�s The Great Gatsby in which a character, Tom Buchanan, states: �Have you read The Rise of the Colored Empires by this man Goddard?� � Well, it�s a fine book, and everybody ought to read it. The idea is if we don�t look out the white race will be�will be utterly submerged. It�s all scientific stuff; it�s been proved.� Buchanan�s comment is a thinly veiled reference to Lothrop Stoddard�s The Rising Tide of Color which Hsu describes as �rationalized hatred� presented in a scholarly, gentlemanly, and scientific tone. (This wording that will certainly help him when he comes up for tenure.) As Hsu notes, Stoddard had a doctorate from Harvard and was a member of many academic associations. His book was published by a major publisher. It was therefore �precisely the kind of book that a 1920s man of Buchanan�s profile � wealthy, Ivy League�educated, at once pretentious and intellectually insecure � might have been expected to bring up in casual conversation.� Let�s ponder that a bit. The simple reality is that in the year 2009 an Ivy League-educated person, "at once pretentious and intellectually insecure," would just as glibly assert the same sort of nonsense as Hsu. To wit: The coming white minority does not mean that the racial hierarchy of American culture will suddenly become inverted, as in 1995�s White Man�s Burden, an awful thought experiment of a film, starring John Travolta, that envisions an upside-down world in which whites are subjugated to their high-class black oppressors. There will be dislocations and resentments along the way, but the demographic shifts of the next 40 years are likely to reduce the power of racial hierarchies over everyone�s lives, producing a culture that�s more likely than any before to treat its inhabitants as individuals, rather than members of a caste or identity group. The fact is that no one can say for certain what multicultural America without a white majority will be like. There is no scientific or historical basis for claims like �the demographic shifts of the next 40 years are likely to reduce the power of racial hierarchies over everyone�s lives, producing a culture that�s more likely than any before to treat its inhabitants as individuals, rather than members of a caste or identity group.� Indeed, there is no evidence at all that we are proceeding to a color blind future. The election results continue to show that white people are coalescing in the Republican Party, while the Democrats are increasingly the party of a non-white soon-to-be majority. Is it so hard to believe that when this coalition achieves a majority that it will further compromise the interests of whites far beyond contemporary concerns such as immigration policy and affirmative action? Hsu anticipates a colorblind world, but affirmative action means that blacks and other minorities are certainly not treated as individuals. And it means that whites � especially white males � are losing out on opportunities they would have had without these policies and without the massive non-white immigration of the last few decades. Given the intractability of changing intelligence and other traits required for success in the contemporary economy, it is unlikely that 40 more years of affirmative action will attain the outcomes desired by the minority lobbies. Indeed, in Obama's America, blacks are rioting in Oakland over perceived racial injustices, and from 2002 �2007, black juvenile homicide victims increased 31%, while black juvenile homicide perpetrators increased 43%. Hence, the reasonable outlook is for a continuing need for affirmative action and for racial activism in these groups, even after whites become a minority. Whites will also lose out because of large-scale importation of relatively talented immigrants from East Asia. Indeed, as I noted over a decade ago, "The United States is well on the road to being dominated by an Asian technocratic elite and a Jewish business, professional, and media elite." Hsu shows that there already is considerable anxiety among whites about the future. An advertizing executive says, �I think white people feel like they�re under siege right now � like it�s not okay to be white right now, especially if you�re a white male. ... People are stressed out about it. �We used to be in control! We�re losing control�� Another says, "There�s a lot of fear and a lot of resentment." It's hard to see why these feelings won't increase in the future. A huge problem for white people is lack of intellectual and cultural confidence. Hsu quotes Christian (Stuff White People Like) Lander saying, "I get it: as a straight white male, I�m the worst thing on Earth." A professor comments that for his students "to be white is to be culturally broke. The classic thing white students say when you ask them to talk about who they are is, �I don�t have a culture.� They might be privileged, they might be loaded socioeconomically, but they feel bankrupt when it comes to culture � They feel disadvantaged, and they feel marginalized." This lack of cultural confidence is no accident. For nearly 100 years whites have been subjected to a culture of critique emanating from the most prestigious academic and media institutions. And, as Hsu points out, the most vibrant and influential aspect of American popular culture is hip-hop�a product of the African American urban culture. The only significant group of white people with any cultural confidence centers itself around country music, NASCAR, and the small town values of traditional white America. For this group of whites � and only this group � there is "a racial pride that dares not speak its name, and that defines itself through cultural cues instead�a suspicion of intellectual elites and city dwellers, a preference for folksiness and plainness of speech (whether real or feigned), and the association of a working-class white minority with 'the real America.'� This is what I term implicit whiteness � implicit because explicit assertions of white identity have been banned by the anti-white elites that dominate our politics and culture. It is a culture that, as Hsu notes, "cannot speak its name." But that implies that the submerged white identity of the white working class and the lack of cultural confidence exhibited by the rest of white America are imposed from outside. Although there may well be characteristics of whites that facilitate this process, this suppression of white identity and interests is certainly not the natural outcome of modernization or any other force internal to whites as a people. In my opinion, it is the result of the successful erection of a culture of critique in the West dominated by Jewish intellectual and political movements. The result is that educated, intellectually insecure white people these days are far more likely to believe in the utopian future described by Hsu than in hard and cautious thinking about what the future might have in store for them. It's worth dwelling a bit on the intellectual insecurity of the whites who mindlessly utter the mantras of multiculturalism that they have soaked up from the school system and from the media. Most people do not have much confidence in their intellectual ability and look to elite opinion to shape their beliefs. As I noted elsewhere, A critical component of the success of the culture of critique is that it achieved control of the most prestigious and influential institutions of the West, and it became a consensus among the elites, Jewish and non-Jewish alike. Once this happened, it is not surprising that this culture became widely accepted among people of very different levels of education and among people of different social classes. Most people are quite insecure about their intellectual ability. But they know that the professors at Harvard, and the editorial page of the New York Times and the Washington Post, and even conservative commentators like Rush Limbaugh and Sean Hannity are all on page when it comes to racial and ethnic issues. This is a formidable array, to the point that you almost have to be a crank to dissent from this consensus. I think one of the greatest triumphs of the left has been to get people to believe that people who assert white identity and interests or who make unflattering portrayals of organized Jewish movements are morally degenerate, stupid, and perhaps psychiatrically disturbed. Obviously, all of these adjectives designate low status. The reality is that the multicultural emperor has no clothes and, because of its support for racial Zionism and the racialism of ethnic minorities in America, it is massively hypocritical to boot. The New York Times, the academic left, and the faux conservatives that dominate elite discourse on race and ethnicity are intellectually bankrupt and can only remain in power by ruthlessly suppressing or ignoring the scientific findings. This is particularly a problem for college-educated whites. Like Fitzgerald's Tom Buchanan, such people have a strong need to feel that their ideas are respectable and part of the mainstream. But the respectable mainstream gives them absolutely nothing with which to validate themselves except perhaps the idea that the world will be a better place when people like them no longer have power. Hsu quotes the pathetic Christian Lander: "�Like, I�m aware of all the horrible crimes that my demographic has done in the world. ... And there�s a bunch of white people who are desperate � desperate � to say, �You know what? My skin�s white, but I�m not one of the white people who�s destroying the world.�� As a zombie leftist during the 1960s and 1970s, I know what that feeling of desperation is like � what it's like to be a self-hating white. We must get to the point where college-educated whites proudly and confidently say they are white and that they do not want to become a minority in America. This reminds me of the recent docudrama Milk, which depicts the life of gay activist Harvey Milk. Milk is sure be nominated for an Oscar as Best Picture because it lovingly illustrates a triumph of the cultural left. But is has an important message that should resonate with the millions of whites who have been deprived of their confidence and their culture: Be explicit. Just as Harvey Milk advocated being openly gay even in the face of dire consequences, whites need to tell their family and their friends that they have an identity as a white person and believe that whites have legitimate interests as white people. They must accept the consequences when they are harassed, fired from their jobs, or put in prison for such beliefs. They must run for political office as openly pro-white. Milk shows that homosexuals were fired from their jobs and arrested for congregating in public. Now it's the Southern Poverty Law Center and the rest of the leftist intellectual and political establishment that harasses and attempts to get people fired. But it's the same situation with the roles reversed. No revolution was ever accomplished without some martyrs. The revolution that restores the legitimacy of white identity and the legitimacy of white interests will be no exception. But it is a revolution that is absolutely necessary. The white majority is foolish indeed to entrust its future to a utopian hope that racial and ethnic identifications will disappear and that they won�t continue to influence public policy in ways that compromise the interests of whites. It does not take an overactive imagination to see that coalitions of minority groups could compromise the interests of formerly dominant whites. We already see numerous examples in which coalitions of minority groups attempt to influence public policy, including immigration policy, against the interests of the whites. Placing ourselves in a position of vulnerability would be extremely risky, given the deep sense of historical grievance fostered by many ethnic activists and organized ethnic lobbies. This is especially the case with Jews. Jewish organisations have been unanimous in condemning Western societies, Western traditions, and Christianity, for past crimes against Jews. Similar sentiments are typical of a great many African Americans and Latinos, and especially among the ethnic activists from these groups. The �God damn America� sermon by President Obama's pastor comes to mind as a recent notorious example. The precedent of the early decades of the Soviet Union should give pause to anyone who believes that surrendering ethnic hegemony does not carry risks. The Bolshevik revolution had a pronounced ethnic angle: To a very great extent, Jews and other non-Russians ruled over the Russian people, with disastrous consequences for the Russians and other ethnic groups that were not able to become part of the power structure. Jews formed a hostile elite within this power structure � as they will in the future white-minority America; Jews were �Stalin�s willing executioners.� Two passages from my review of Yuri Slezkine's The Jewish Century seem particularly appropriate here. The first passage reminds me of the many American Jews who adopt a veneer of support for leftist versions of social justice and racial tolerance while nevertheless managing to support racial Zionism and the mass murder, torture, and incarceration of the Palestinian people in one of the largest prison systems the world has ever seen. Such people may be very different when they become a hostile elite in a white-minority America. Many of the commentators on Jewish Bolsheviks noted the �transformation� of Jews [after the Bolshevik Revolution]. In the words of [a] Jewish commentator, G. A. Landau, �cruelty, sadism, and violence had seemed alien to a nation so far removed from physical activity.� And another Jewish commentator, Ia. A. Bromberg, noted that: the formerly oppressed lover of liberty had turned into a tyrant of �unheard-of-despotic arbitrariness��. The convinced and unconditional opponent of the death penalty not just for political crimes but for the most heinous offenses, who could not, as it were, watch a chicken being killed, has been transformed outwardly into a leather-clad person with a revolver and, in fact, lost all human likeness. ... After the Revolution, ... there was active suppression of any remnants of the older order and their descendants. ... The mass murder of peasants and nationalists was combined with the systematic exclusion of the previously existing non-Jewish middle class. The wife of a Leningrad University professor noted, �in all the institutions, only workers and Israelites are admitted; the life of the intelligentsia is very hard� (p. 243). Even at the end of the 1930s, prior to the Russification that accompanied World War II, �the Russian Federation�was still doing penance for its imperial past while also serving as an example of an ethnicity-free society� (p. 276). While all other nationalities, including Jews, were allowed and encouraged to keep their ethnic identities, the revolution remained an anti-majoritarian movement. The difference from the Soviet Union may well be that in white-minority America it will not be workers and Israelites who are favored, but non-whites and Israelites. Whites may dream that they are entering the post-racial utopia imagined by their erstwhile intellectual superiors. But it is quite possible that they are entering into a racial dystopia of unimaginable cruelty in which whites will be systematically excluded in favor of the new elites recruited from the soon-to-be majority. It's happened before. Kevin MacDonald is a professor of psychology at California State University�Long Beach. Permanent URL with hyperlinks: http://www.theoccidentalobserver.net/articles/MacDonald-Hsu.html ----------- Should Christians Support Israeli Terrorism in Gaza? A timely discussion between Rev. Ted Pike and Dr. David Duke, one especially important for the Christians in our audience http://www.davidduke.com/mp3/dukeradio090122DukeandPikeonGaza.mp3 In this vital discussion, Rev. Pike and Dr. Duke explore the Pro-Israel attitude of some Christian evangelical organizations, and why their position not only goes directly against Christian morality and decency, but actually is directly opposite of that expressed by Christian Scriptures. Today, Many Christians are instructed that Jews and today�s Israel has a special covenant� with God. In fact, the New Testament in the clearest of language states that the Jews �continued not in my covenant, and I considered them not, saith the Lord.� Here�s the quote that Christians aren�t supposed to notice.: 8:10 Not according to the covenant that I made with their fathers, in the day when I took them by the hand out of the land of Egypt; because they continued not in my covenant, and I regarded them not, saith the Lord. (Hebrews 8:10) They also don�t seem to notice that a 2000 year old Judaic war against Christianity that has been waged since time of Jesus Christ and still goes on today with the most powerful Jewish organizations attempting to destroy European and American traditions, that has even become a war on our Christmas traditions. Dr. Duke and Ted Pike also speak about how over a hundred thousand Christian Palestinians have suffered with their families from anti-Christian Israel! Christian support of Israel has resulted in the very birthplace of Jesus Christ, go from 90 percent Palestinian Christians to 35 percent today because of Israeli terror and occupation. They ask, �How could any Christian in good conscience support the anti-Christian state of Israel, bombing the homes, killing and maiming, torturing and oppressing fellow Christian men, women and children?� This is a vital show for every Christian reader and listener of DavidDuke.com. Next time, you hear someone say, �God tells us that we must support Israel� you will have the clear Christian answer that just the opposite is true! For documentation on this be sure to read some of the well-footnoted, sample chapters of Jewish Supremacism and My Awakening. Source : http://www.davidduke.com/general/should-christians-support-israeli-terroris… ------------------------------------- You or someone using your email adress is currently subscribed to the Lawrence Auster Newletter. If you wish to unsubscribe from our mailing list, please let us know by calling to 1 212 865 1284 Thanks, Lawrence Auster, 238 W 101 St Apt. 3B New York, NY 10025 Contact: lawrence.auster(a)att.net -------------------------------------

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[Clarity-cvs] r1 - doc doc/html doc/html/dictionary doc/html/images gui gui/icons sql utilities utilities/delivery
by skleinberg＠common-lisp.net 16 Aug '06

16 Aug '06

Author: skleinberg Date: Wed Aug 16 16:18:39 2006 New Revision: 1 Added: COPYING.txt LGPL.TXT README.txt alignment-functions.lisp.lisp clarity-package.lisp clarity.exe (contents, props changed) clarity.system database-functions.lisp decimal-number.lisp doc/ doc/html/ doc/html/clarity-package.html doc/html/clarity-schema.png (contents, props changed) doc/html/dictionary/ doc/html/dictionary.html doc/html/dictionary/align-charts.html doc/html/dictionary/align-to-consensus.html doc/html/dictionary/alignment-item.html doc/html/dictionary/alignment.html doc/html/dictionary/build-consensus.html doc/html/dictionary/connect.html doc/html/dictionary/ganttify.html doc/html/dictionary/get-all-data.html doc/html/dictionary/get-children.html doc/html/dictionary/get-consensus-terms.html doc/html/dictionary/get-data-terms.html doc/html/dictionary/get-node-terms.html doc/html/dictionary/get-root.html doc/html/dictionary/insert-node.html doc/html/dictionary/insert.html doc/html/dictionary/lastid.html doc/html/dictionary/needleman-wunsch.html doc/html/dictionary/score-pair-consensus.html doc/html/dictionary/score-pair.html doc/html/dictionary/score.html doc/html/dictionary/store-consensus-sequence.html doc/html/dictionary/store-gantt-chart.html doc/html/dictionary/store-gantt-charts.html doc/html/dictionary/store-numerical-data.html doc/html/dictionary/string-alignment.html doc/html/dictionary/tree-insert-recursive.html doc/html/dictionary/tree-insert.html doc/html/downloads.html doc/html/gui.html doc/html/images/ doc/html/images/Thumbs.db (contents, props changed) doc/html/images/interface2.jpg (contents, props changed) doc/html/images/phylogeny-1-smaller.jpg (contents, props changed) doc/html/images/phylogeny-1.jpg (contents, props changed) doc/html/images/phylogeny-2-smaller.jpg (contents, props changed) doc/html/images/phylogeny-2.jpg (contents, props changed) doc/html/images/phylogeny-3.jpg (contents, props changed) doc/html/images/shim.gif (contents, props changed) doc/html/index.html doc/html/installation.html doc/html/links.html doc/html/style.css gui/ gui/clarity-database-setup-interface.lisp gui/clarity-gui.system gui/clarity-interface-functions.lisp gui/clarity-interface.lisp gui/icons/ gui/icons/base.bmp (contents, props changed) gui/icons/down.bmp (contents, props changed) gui/icons/icons.bmp (contents, props changed) gui/icons/inactive.bmp (contents, props changed) gui/icons/neutral.bmp (contents, props changed) gui/icons/up.bmp (contents, props changed) gui/insert-data-interface.lisp gui/start-gui.lisp sql/ sql/clarity.sql utilities/ utilities/delivery/ utilities/delivery/clarity-4.ico (contents, props changed) utilities/delivery/clarity-icon-3.bmp (contents, props changed) utilities/delivery/clarity-icon-3.ico (contents, props changed) utilities/delivery/clarity-icon-4.bmp (contents, props changed) utilities/delivery/clarity-icon-4.ico (contents, props changed) utilities/delivery/clarity.ico (contents, props changed) utilities/delivery/delivery-script.fsl (contents, props changed) utilities/delivery/delivery-script.lisp utilities/delivery/lwdeli.bat Log: Initial import Added: COPYING.txt ============================================================================== --- (empty file) +++ COPYING.txt Wed Aug 16 16:18:39 2006 @@ -0,0 +1,18 @@ +CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. +END OF TERMS AND CONDITIONS \ No newline at end of file Added: README.txt ============================================================================== --- (empty file) +++ README.txt Wed Aug 16 16:18:39 2006 @@ -0,0 +1,22 @@ +CLARITY + +CLARITY is a tool and method for the storage and comparison of data with numeric and set membership components. +It is specifically geared toward timecourse microarray data, which is used to study the activity of genes across time. +By using data that has been redescribed into Gene Ontology (GO) terms, and summarizing the regulation of these terms across +time using characters (together forming sequences) we are able to use standard DNA alignment techniques with these sequences. + +The Gene Ontology (GO), is a controlled vocabulary used to aid the description of genes and gene product attributes in a +variety of organisms. There are three different ontologies that describe molecular functions, biological processes, and cellular components. + +Requirements: + +CLARITY Database -- which requires MySQL. +Lispworks Enterprise Edition 4.2 or higher -- this restriction will +be removed soon by making sure that the MySQL connection works +on the freely available CL-SQL. + + +Last Update: 2006-08-16 + +Contact: samantha AT bioinformatics DOT nyu DOT edu +Copyright 2006 Samantha Kleinberg Added: alignment-functions.lisp.lisp ============================================================================== --- (empty file) +++ alignment-functions.lisp.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,551 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +(eval-when (:compile-toplevel :load-toplevel :execute) + (require "sql") + (require "odbc")) + +#.(sql:enable-sql-reader-syntax) + +(defparameter *gap* #\-) +(defparameter *true* 1) +(defparameter *false* 0) + +(defstruct (alignment + (:constructor new-alignment)) + (score) + (items)) ;;type is pair of alignment items + +(defstruct (alignment-item + (:constructor new-alignment-item)) + (dataset-id) + (chart-id) + (term-name) + (string)) + + +(defgeneric align-charts (clh id_1 id_2) + (:documentation "Aligns two datasets, given their timecourse data ids. + arguments: clarity-handle timecourse-id-1 timecourse-id-2 + usage: (clarity:align-charts clarity-handle timecourse-id-1 timecourse-id-2) + notes: Returns hash table of alignments hashed by score" + )) + +(defgeneric score-pair (clh id_1 id_2) + (:documentation "Given two timecourse data ids, computes their alignment and + returns score computed from hash table +arguments: clarity-handle timecourse-data-id-1 timecourse-data-id-2 +usage: (clarity:score-pair clarity-handle timecourse-data-id-1 timecourse-data-id-2) +notes: Returns single numerical value" + )) + +(defgeneric align-to-consensus (clh timecourse-id consensus-id) + (:documentation "Aligns timecourse data to consensus data" + )) + +(defgeneric string-alignment (string1 string2) + (:documentation "Given two strings, performs dynamic programming alignment and returns the alignment score + arguments: string1 string2 + usage: (clarity:string-alignment ""UUDDUI"" ""IUDDDI"")" + )) + +(defgeneric score (char1 char2) + (:documentation "Given two characters, this function returns the numerical value associated with alignign one to the other + arguments: character1 character2 + usage (clarity:score U D)" + )) + +(defgeneric get-root (clh) + (:documentation "Returns root of phylogenetic tree. + arguments: clarity-handle + usage: (clarity:get-root clarity-handle) + notes: returns id number of root node." + )) + +;;right now, choose charts based on data ids +(defmethod align-charts ((clh clarity-handle) id_1 id_2) + ;;get intersection of datasets + (let* ((alignment-hash (make-hash-table :test #'equal)) + (intersection-list (sql:select [fir.term_name] [fir.timecourse_data_id] [fir.id] [fir.sequence] + [sec.timecourse_data_id] [sec.id] [sec.sequence] + :from '(#.(sql::make-db-identifier :val "gantt_chart FIR") + #.(sql::make-db-identifier :val "gantt_chart SEC")) + :where [and [= ["FIR" timecourse_data_id] id_1] + [= ["SEC" timecourse_data_id] id_2] + [= ["FIR" term_name] ["SEC" term_name]]] + :database (connection clh) + )) + (alignment-items (loop for (term time_id_1 first_id first_sequence + time_id_2 second_id second_sequence) in intersection-list + collecting (list (new-alignment-item :dataset-id time_id_1 + :chart-id first_id + :term-name term + :string first_sequence) + (new-alignment-item :dataset-id time_id_2 + :chart-id second_id + :term-name term + :string second_sequence)) + ))) + + (loop for value in (loop for (left right) in alignment-items + collecting (new-alignment :score (string-alignment + (alignment-item-string left) + (alignment-item-string right)) + :items (list left right)) + ) + do (push value (gethash (alignment-score value) alignment-hash)) + finally (return alignment-hash)) + )) + + +(defmethod score-pair ((clh clarity-handle) id_1 id_2) + (let ((hash (align-charts clh + (first (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] id_1] + :database (connection clh)))) + (first (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] id_2] + :database (connection clh))))))) + (loop for key being the hash-keys of hash + with alignmentSum=0 + summing (* key (length (gethash key hash))) into alignmentSum + finally (return alignmentSum) + )) + ) + + +(defmethod align-to-consensus ((clh clarity-handle) timecourse-id consensus-id) + ;;get intersection of datasets + (let* ((alignment-hash (make-hash-table :test #'equal)) + (intersection-list (sql:select [fir.term_name] [fir.timecourse_data_id] [fir.id] [fir.sequence] + [sec.tree_id] [sec.id] [sec.sequence] + :from '(#.(sql::make-db-identifier :val "gantt_chart FIR") + #.(sql::make-db-identifier :val "consensus SEC")) + :where [and [= ["FIR" timecourse_data_id] timecourse-id] + [= ["SEC" tree_id] consensus-id] + [= ["FIR" term_name] ["SEC" term_name]]] + :database (connection clh) + )) + + (alignment-items (loop for (term time_id first_id first_sequence + tree_id second_id second_sequence) in intersection-list + collecting (list (new-alignment-item :dataset-id time_id + :chart-id first_id + :term-name term + :string first_sequence) + (new-alignment-item :dataset-id tree_id + :chart-id second_id + :term-name term + :string second_sequence)) + ))) + + (loop for value in (loop for (left right) in alignment-items + collecting (new-alignment :score (string-alignment + (alignment-item-string left) + (alignment-item-string right)) + :items (list left right)) + ) + do (push value (gethash (alignment-score value) alignment-hash)) + finally (return alignment-hash)) + )) + +(defmethod score-pair-consensus ((clh clarity-handle) timecourse-id consensus-id) + (let ((hash (align-to-consensus clh + (first (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] timecourse-id] + :database (connection clh)))) + consensus-id))) + + + (loop for key being the hash-keys of hash + with alignmentSum=0 + summing (* key (length (gethash key hash))) into alignmentSum + finally (return alignmentSum) + ) + ) + ) + + +(defmethod score (char1 char2) + (declare (type character char1 char2)) + (cond ((char= char1 char2) 3) + ;((char= char1 *gap*) -1) + ;((char= char2 *gap*) -1) + ((and (char= char1 #\U) (char= char2 #\D)) -2) + ((and (char= char1 #\D) (char= char2 #\U)) -2) + (t -1) + )) + +(defmethod string-alignment (string1 string2) + (let* ((l1 (length string1)) + (l2 (length string2)) + (table (make-array (list (+ l1 1) (+ l2 1)) + :initial-element 0))) + + ;;initialize table + (loop for i from 1 to l1 + do (setf (aref table i 0) (+ (aref table (- i 1) 0) (score (char string1 (- i 1)) *gap*))) + ) + (loop for k from 1 to l2 + do (setf (aref table 0 k) (+ (aref table 0 (- k 1)) (score *gap* (char string2 (- k 1)))))) + + ;;fill in rest of table and return score in lower right corner + (loop for k from 1 to l2 + do (loop for i from 1 to l1 + do (setf (aref table i k) + (max (+ (aref table (- i 1) k) (score (char string1 (- i 1)) *gap*)) + (+ (aref table (- i 1) (- k 1)) (score (char string1 (- i 1)) + (char string2 (- k 1)))) + (+ (aref table i (- k 1)) (score *gap* (char string2 (- k 1))))))) + finally (return (aref table l1 l2 ))) + + )) + + + + +(defmethod get-root ((clh clarity-handle)) + ;;returns tree id of root node + (first (sql:with-transaction + (sql:select [id] + :from [|tree|] + :where [= [is_root] 1] + :database (connection clh) + :flatp t)))) + + + +(defmethod tree-insert ((clh clarity-handle) timecourse_data_id) + (let ((root (get-root clh))) + (if root + ;there is a root + (let ((new-node-id)) + ;;make node for new-node + (sql:with-transaction + (sql:insert-records :into [|tree|] + :attributes '([|timecourse_data_id|] [|node_left|] [|node_right|]) + :values (list timecourse_data_id 0 0) + :database (connection clh))) + (setf new-node-id (lastid clh :table "tree")) + (setf *new-best-node* 0) + (setf *new-best-score* 0) + + (multiple-value-bind (best-node best-score) + (tree-insert-recursive clh new-node-id root) + ;;if there is no best node, insert as sibling of root + (insert-node clh new-node-id + (cond ((= best-node 0) root) + (t best-node))))) + + ;no root, data to insert becomes root. this is the base case + (sql:with-transaction + (sql:insert-records :into [|tree|] + :attributes '([|timecourse_data_id|] + [|is_root|] + [|node_left|] + [|node_right|]) + :values (list timecourse_data_id *true* 0 0) + :database (connection clh))) + ) + )) + + +;;node referred to by node-id. if node has no children, it has timecourse data. +;; if it's an internal node, it has simply a consensus sequence" + +(defvar *new-best-node*) +(defvar *new-best-score*) + +(defmethod tree-insert-recursive ((clh clarity-handle) new-node current-node) + #| (if (eq depth 0) + (score-pair clh new-node current-node) + )|# + (destructuring-bind (left right) + (first (sql:select [node_left] [node_right] + :from [|tree|] + :where [= [id] current-node] + :database (connection clh))) + (let ((score (cond ((and (= 0 left) (= 0 right)) ;;if leaf node, use reg-score-pair + (score-pair clh new-node current-node)) + (t (score-pair-consensus clh new-node current-node)))) +; (new-best-node best-node) + ; (new-best-score best-score)) + ) + + (when (> score *new-best-score*) + (setf *new-best-node* current-node) + (setf *new-best-score* score) + ) + + (if (> left 0) + (tree-insert-recursive clh new-node left)) + + (if (> right 0) + (tree-insert-recursive clh new-node right)) + + (values *new-best-node* *new-best-score*) + ))) + + + +(defmethod insert-node ((clh clarity-handle) new-node-id sibling-node-id) + (let ((new-parent-id) + (new-node-data-id (first (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] new-node-id] + :database (connection clh))))) + (new-consensus)) + + (destructuring-bind (sib-left sib-right sib-data-id is-root) + (first (sql:select [node_left] [node_right][timecourse_data_id][is_root] + :from [|tree|] + :where [= [|id|] sibling-node-id] + :database (connection clh) + )) + + (when is-root + ;;if sibling was root, it no longer is, then parent becomes root + (sql:update-records [|tree|] + :where [= [|id|] sibling-node-id] + :attributes '([|is_root|]) + :values '(0) + :database (connection clh)) + ) + + ;;make new-node for parent + (sql:with-transaction + (sql:insert-records :into [|tree|] + :attributes '([|timecourse_data_id|] [|node_left|] [|node_right|][is_root]) + :values (list 0 sibling-node-id new-node-id is-root) + :database (connection clh))) + + (setf new-parent-id (lastid clh :table "tree")) + ;;update parent's consensus seq with it's id + ;;actualyl consensus id IS node id! + + ;;update sibling's original parent + ;;could have been a left child or a right child. try both. + ;;get id to update old parent's consensus + (let ((old-parent-id + (or (first (sql:with-transaction + (sql:select [|id|] :from [|tree|] + :where [and [= [node_left] sibling-node-id] + [not [= [id] new-parent-id]]] + :database (connection clh) :flatp t))) + (first (sql:with-transaction + (sql:select [|id|] :from [|tree|] + :where [and [= [node_right] sibling-node-id] + [not [= [id] new-parent-id]]] + :database (connection clh) :flatp t)))))) + (sql:with-transaction + (sql:update-records [|tree|] + :where [and [= [node_left] sibling-node-id] + [= [id] old-parent-id]] + :attributes '([|node_left|]) + :values (list new-parent-id) + :database (connection clh))) + + (sql:with-transaction + (sql:update-records [|tree|] + :where [and [= [node_right] sibling-node-id] + [= [id] old-parent-id]] + :attributes '([|node_right|]) + :values (list new-parent-id) + :database (connection clh))) + + + + ;;build consensus sequence + ;;when buildng consensus: right is always real data, since new. left may or may not be consensus + (build-consensus clh new-parent-id sibling-node-id new-node-data-id) + + + (when old-parent-id + ;;after making consensus sequence, for new node, need to update parent of new node's consensus! + ;;delete old consensus from table + (sql:with-transaction + (sql:delete-records :from [|consensus|] + :where [= [tree_id] old-parent-id] + :database (connection clh))) + + ;;build consensus to replace old + (build-internal-consensus clh old-parent-id)) + + + )))) + + +(defvar *test*) +(defvar *test-list*) + +(defmethod build-consensus ((clh clarity-handle) node-id data-left data-right) + ;;right is always timecourse, left may be either + + (destructuring-bind (data-id) + (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] data-left] + :database (connection clh))) + (let ((term-seq-list + (cond ((> data-id 0) + ;;if left is timecourse_data + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "gantt_chart LCHILD") + #.(sql::make-db-identifier :val "gantt_chart RCHILD")) + :where [and [= ["LCHILD" timecourse_data_id] data-id] + [= ["RCHILD" timecourse_data_id] data-right] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + ; ((> consensus-id 0) + ;;left is consensus data + (t + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "consensus LCHILD") + #.(sql::make-db-identifier :val "gantt_chart RCHILD")) + :where [and [= ["LCHILD" tree_id] data-left] + [= ["RCHILD" timecourse_data_id] data-right] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + #|(t + (print "error!!!"))|# + ))) + + (setf *test-list* term-seq-list) + + (when term-seq-list + (loop for (term seq) in term-seq-list + do(store-consensus-sequence clh node-id term seq) + )) + + ))) + +(defmethod build-internal-consensus ((clh clarity-handle) node-id) + ;;at least one node is consensus, other may be either + (destructuring-bind (data-left data-right) + (first (sql:select [|node_left|] [|node_right|] + :from [|tree|] + :where [= [|id|] node-id] + :database (connection clh))) + + (let ((left-data-id + (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] data-left] + :database (connection clh) + :flatp t))) + (right-data-id + (first (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] data-right] + :database (connection clh) + :flatp t)))) + (let ((term-seq-list + (cond ((and (> left-data-id 0) + (> right-data-id 0)) + ;;if left is timecourse_data + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "gantt_chart LCHILD") + #.(sql::make-db-identifier :val "gantt_chart RCHILD")) + :where [and [= ["LCHILD" timecourse_data_id] left-data-id] + [= ["RCHILD" timecourse_data_id] right-data-id] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + ((and (> left-data-id 0) + (= right-data-id 0)) + ;;if left is timecourse_data + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "gantt_chart LCHILD") + #.(sql::make-db-identifier :val "consensus RCHILD")) + :where [and [= ["LCHILD" timecourse_data_id] left-data-id] + [= ["RCHILD" tree_id] data-right] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + + ((and (= left-data-id 0) + (= right-data-id 0)) + ;;if left is timecourse_data + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "consensus LCHILD") + #.(sql::make-db-identifier :val "consensus RCHILD")) + :where [and [= ["LCHILD" tree_id] data-left] + [= ["RCHILD" tree_id] data-right] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + + (t + (sql:select [lchild.term_name] [lchild.sequence] + :from '(#.(sql::make-db-identifier :val "consensus LCHILD") + #.(sql::make-db-identifier :val "gantt_chart RCHILD")) + :where [and [= ["LCHILD" tree_id] data-left] + [= ["RCHILD" timecourse_data_id] right-data-id] + [= ["LCHILD" term_name] ["RCHILD" term_name]] + [= ["LCHILD" sequence] ["RCHILD" sequence]]] + :database (connection clh))) + ))) + + term-seq-list + (when term-seq-list + (loop for (term seq) in term-seq-list + do(store-consensus-sequence clh node-id term seq) + )) + + )))) + +(defmethod store-consensus-sequence ((clh clarity-handle) node-id term-name sequence) + (sql:with-transaction + (sql:insert-records :into [|consensus|] + :attributes '([|tree_id|] [|term_name|] [|sequence|]) + :values (list node-id term-name sequence) + :database (connection clh))) + ) + +(defmethod get-consensus-terms ((clh clarity-handle) node-id) + ;;node-id is tree id + (sql:with-transaction + (sql:select [term_name] + :from [|consensus|] + :where [= [tree_id] node-id] + :database (connection clh))) + ) + +(defmethod get-data-terms ((clh clarity-handle) data-id) + (sql:with-transaction + (sql:select [term_name] + :from [|gantt_chart|] + :where [= [timecourse_data_id] data-id] + :database (connection clh))) + + ) + +#.(sql:disable-sql-reader-syntax) + + +;;; end of file -- alignment-functions.lisp -- Added: clarity-package.lisp ============================================================================== --- (empty file) +++ clarity-package.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,113 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(defpackage "CLARITY" (:use "CL") + (:export + "ALIGN-CHARTS" + "SCORE" + "SCORE-PAIR" + "ALIGN-TO-CONSENSUS" + "SCORE-PAIR-CONSENSUS" + "STRING-ALIGNMENT" + "GET-ROOT" + + "TREE-INSERT" + "TREE-INSERT-RECURSIVE" + "INSERT-NODE" + "BUILD-CONSENSUS" + "BUILD-INTERNAL-CONSENSUS" + "STORE-CONSENSUS-SEQUENCE" + "GET-CONSENSUS-TERMS" + "GET-DATA-TERMS") + (:export + "CLARITY-HANDLE" + "CLARITY-HANDLE-P" + "*CURRENT-CLARITY-HANDLE*" + "MAKE-CLARITY-HANDLE" + "DISCONNECT-CLARITY-DBS" + "CONNECT" + "NUMBER-TO-STRING" + "INSERT" + "INSERT-WITH-PROBES" + "GANTTIFY" + "GANTTIFY-WITH-PROBES" + "STORE-GANTT-CHARTS" + "STORE-GANTT-CHART" + "STORE-NUMERICAL-DATA" + "STORE-NUMERICAL-AND-PROBE-DATA" + "FLATTEN" + "LASTID" + "FILE-LINES" + "GET-CHILDREN" + "GET-NODE-TERMS" + "GET-ALL-DATA") + + (:export + "READ-STRING-WHILE" + "DECIMAL-READER" + "PARSE-DECIMAL" + "USE-DECIMAL") + + (:export + "INSERT-FILE-POPUP" + "GET-FILENAME" + "DATABASE-SWITCH-CALLBACK" + "PRINT-PARTIAL-FILENAME" + ) + (:export + "START-CLARITY-GUI" + "START-SETUP-INTERFACE" + ) + + (:export + "*CLARITY-DB-NAME*" + "*CLARITY-DB-USER*" + "*CLARITY-DB-PASSWORD*" + ) + + (:export + "INSERT-FILE-POPUP" + "INSERT-DATA-INTERFACE" + "GET-FILENAME" + "GET-PHYLOGENY-ROOT" + "GET-PHYLOGENY-CHILDREN" + "DATABASE-SWITCH-CALLBACK" + "PRINT-PARTIAL-FILENAME" + ) + (:export + "START-CLARITY-GUI" + "START-CLARITY-INTERFACE" + "START-SETUP-INTERFACE" + "START-WINDOWS-DATA-SOURCE-SETUP" + "START-MACOSX-DATA-SOURCE-SETUP" + "CLARITY-DATABASE-SETUP-INTERFACE" + ) + (:export + "PHYLOGENY-ITEM" + "PHYLOGENY-TERM" + "PHYLOGENY-WINDOW" + ) + ) + + + + +;;; end of file -- clarity-package.lisp -- Added: clarity.exe ============================================================================== Binary file. No diff available. Added: clarity.system ============================================================================== --- (empty file) +++ clarity.system Wed Aug 16 16:18:39 2006 @@ -0,0 +1,62 @@ +;;; -*- Mode: Lisp -*- + + +;;; Setting up the logical pathname. + +(eval-when (:load-toplevel :execute) + (setf (logical-pathname-translations "CLARITY") + `(("*.*" ,(make-pathname :name :wild :type :wild + :defaults *load-pathname*)) + ("*.*.*" ,(make-pathname :name :wild :type :wild :version :wild + :defaults *load-pathname*)) + ("**;*.*" ,(merge-pathnames + (make-pathname :directory '(:relative :wild-inferiors) + :name :wild + :type :wild + :version :wild) + *load-pathname* + )) + ("**;*.*.*" ,(merge-pathnames + (make-pathname :directory '(:relative :wild-inferiors) + :name :wild + :type :wild + :version :wild + :version :wild) + *load-pathname* + )) + ))) + + + +;;; Adding registry locations. + +(eval-when (:load-toplevel :execute) + (mk:add-registry-location + (merge-pathnames (pathname "gui/") + (make-pathname :name nil :type nil + :defaults *load-pathname*))) + + (mk:add-registry-location (translate-logical-pathname "CLARITY:"))) + + +(mk:defsystem "CLARITY" + :components ("clarity-package" + (:system "cl-data-files") + "decimal-number" + (:file "database-functions" :depends-on ("clarity-package")) + "alignment-functions" + ) + ) + + +#+sysdeps +(mk:defsystem "CLARITY" + :components ((:subsystem "clarity-gui" :source-pathname "gui/") + "decimal-number" + "database-functions" + "alignment-functions" + "cl-data-files" + "clarity-package") + :depends-on ("CL-DATA-FILES")) + +;;; end of file -- clarity.system -- Added: database-functions.lisp ============================================================================== --- (empty file) +++ database-functions.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,465 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +(eval-when (:compile-toplevel :load-toplevel :execute) + (require "sql") + (require "odbc")) + + +#.(sql:enable-sql-reader-syntax) + + +(defclass clarity-handle () + ( + ;; GRAPH/DB maintainance. + ;; none yet + ;; Connection information. + (connection :accessor connection :initform nil) + ) + (:documentation "The CLARITY Handle Class. +Class containing specifications for connecting to the database.")) + + + + +;;; Protocol. + +(defgeneric clarity-handle-p (x) + (:method ((x clarity-handle)) t) + (:method ((x t)) nil)) + +(defgeneric connect (clarity-handle db-spec &optional connection) + (:documentation "Sets up a connection to an the clarity database + for the handle. + arguments: connection string, optional connection + usage: (godb:connect ""data source name/user/password"") + notes: ")) + +(defgeneric insert (clarity-handle filename filedate) + (:documentation "Takes a file and adds it to the database + arguments: handle, path to file, date of file creation + usage: (clarity:insert cl-handle ""Z:/filename.txt"" MO/DAY/YR)" + )) + + +(defgeneric ganttify (clarity-handle filename) + (:documentation "Takes a file with columns of numerical data and transforms + data into strings + arguments: clarity-handle filename + usage: (clarity:ganttify cl-handle ""Z:/filename.txt)" + )) + +(defgeneric get-children (node-id) + (:documentation "Gets left and right child of node in phylogenetic tree + arguments: tree-id + usage: (clarity:get-children tree-id)" + )) + + +(defgeneric get-node-terms (clarity-handle node-id) + (:documentation "Gets all terms associated with a tree node. + arguments: cl-handle tree-id + usage: (clarity:get-node-terms cl-handle tree-id) + notes: Terms may be part of conensus sequence or actual data set" + )) + + +(defun sqlcon () + "Connects to sql using stored connection information." + (sql:connect "GODB_internal/root" :database-type :odbc :if-exists :old)) + + + + +(defvar *cl-handle*) + +(defvar *current-clarity-handle* nil) + +(defun make-clarity-handle () + "Creates a new instance of the clarity handle class and assigns +it to the current-clarity-handle variable" + (setf *current-clarity-handle* (make-instance 'clarity-handle))) + + +(defun disconnect-clarity-dbs () + (when (member (connection *current-clarity-handle*) (sql:connected-databases)) + (sql:disconnect :database (connection *current-clarity-handle*)))) + + +(defmethod connect ((clh clarity-handle) (db-spec string) &optional connection) + (format t "~S connecting as ~S~%" clh db-spec) + (if connection + (setf (connection clh) connection) + (setf (connection clh) (sql:connect db-spec :database-type :odbc :if-exists :old)))) + + +(defun number-to-string (number) + (format nil "~s" number) + ) + +;;will have variety of insert methods, for different types of input. +;;for now, only simple, very processed, input is allowed +(defmethod insert ((clh clarity-handle) filename filedate) + (let ((gantt-chart) + (file-id)) + ;;insert datafile in db + (sql:with-transaction + (sql:insert-records :into [|timecourse_data|] + :attributes '([|datafile_path|] [|creation_date|]) + :values (list filename filedate) + :database (connection clh))) + (setf file-id (lastid clh :table "timecourse_data")) + + ;:Create gantt chart of datafile's contents + (multiple-value-bind (header gantt-chart) (ganttify clh filename) + (store-gantt-charts clh file-id gantt-chart) + (store-numerical-data clh file-id filename) + ) + ;;ask if file should be inserted into tree + (when (capi:confirm-yes-or-no "Add new file to tree?") + (tree-insert clh file-id) + ) + + ) + ) + +(defmethod insert-with-probes ((clh clarity-handle) filename filedate &key probes-p) + (let ((gantt-chart) + (file-id)) + ;;insert datafile in db + (sql:with-transaction + (sql:insert-records :into [|timecourse_data|] + :attributes '([|datafile_path|] [|creation_date|]) + :values (list filename filedate) + :database (connection clh))) + (setf file-id (lastid clh :table "timecourse_data")) + + ;:Create gantt chart of datafile's contents + (multiple-value-bind (header gantt-chart) + (ganttify-with-probes clh filename) + (store-gantt-charts clh file-id gantt-chart) + + (store-numerical-and-probe-data clh file-id filename) + ) + ;;ask if file should be inserted into tree + (when (capi:confirm-yes-or-no "Add new file to tree?") + (tree-insert clh file-id) + ) + + )) + +(defvar numlines) + +(defmethod ganttify ((clh clarity-handle) f) ;clh = clarity handle + (let* ((lines (file-lines f)) + (split-lines (loop for line in lines + collecting (split-sequence:split-sequence #\Tab line :remove-empty-subseqs t) + )) + (head (first split-lines)) + #|header of form "term_name 0 2 TAB 2 4 TAB 4 8 + want '(term name ('(0 2) . . .'(4 8)))|# + (header (append (list (first head)) + (loop for nums in (rest head) + collecting + (loop for dig in (split-sequence:split-sequence #\Space nums :remove-empty-subseqs t) + collecting (cond ((equal dig nil) nil) + (t (coerce (parse-decimal dig) 'double-float))))))) + (numerical-lines (loop for (label . nums) in (rest split-lines) + collecting (append (list label) + (loop for n in nums collecting (cond ((equal n "NIL") nil) + (t (coerce (parse-decimal n) 'double-float))))))) + + (sequences (loop for (label . nums) in numerical-lines + collecting (append (list label) + (list (loop for num in nums + collecting (cond ((equal num nil) #\I) ;;check first so there won't be type errors + ((> num 0) #\U) + ((< num 0) #\D) + ((= num 0) #\N) + (t #\I)) into my-string + finally (return (concatenate 'string my-string)))))))) + + (values header sequences) + )) + +(defmethod ganttify-with-probes ((clh clarity-handle) f) ;clh = clarity handle + (let* ((lines (file-lines f)) + (split-lines (loop for line in lines + collecting (split-sequence:split-sequence #\Tab line :remove-empty-subseqs t) + )) + (head (first split-lines)) + (header (remove-if (lambda (x) + (equal x nil)) + (append (list (first head)) + (loop for nums in (rest head) + collecting (cond ((equal nums "NIL") nil) + (t (loop for dig in + (split-sequence:split-sequence #\Space nums :remove-empty-subseqs t) + collecting (cond ((equal dig nil) nil) + (t (coerce (parse-decimal dig) 'double-float)))))))))) + + (numerical-lines (loop for (label . nums) in (rest split-lines) + collecting (append (list label) + (loop for i from 0 to (- (length nums) 1) by 2 + collecting (cond ((equal (nth i nums) "NIL") nil) + (t (coerce (parse-decimal (nth i nums)) + 'double-float))))))) + + (sequences (loop for (label . nums) in numerical-lines + collecting (append (list label) + (list (loop for num in nums + collecting (cond ((equal num nil) #\I) ;;check first so there won't be type errors + ((> num 0) #\U) + ((< num 0) #\D) + ((= num 0) #\N) + (t #\I)) into my-string + finally (return (concatenate 'string my-string)) + ))))) + ) + + + ; paired-lines + (values header sequences) + )) + + +(defmethod store-gantt-charts ((clh clarity-handle) data_id chart-list) + ;;store multiple gantt charts comprising a data set + ;;would be better to use this and not have to specify each col individually + (let ((window-string "")) + + (loop for c in chart-list + do(store-gantt-chart clh data_id c) + ) + )) + + +(defvar *head) + +(defmethod store-numerical-data ((clh clarity-handle) data-id file) + (let* ((lines (file-lines file)) + (split-lines (loop for line in lines + collecting (split-sequence:split-sequence #\Tab line :remove-empty-subseqs t) + )) + (head (first split-lines)) + #|header of form "term_name 0 2 TAB 2 4 TAB 4 8 + want '(term name ('(0 2) . . .'(4 8)))|# + (header (append (list (first head)) + (loop for nums in (rest head) + collecting (loop for dig in (split-sequence:split-sequence #\Space nums :remove-empty-subseqs t) + collecting (coerce (parse-decimal dig) 'short-float))))) + (numerical-lines (loop for (label . nums) in (rest split-lines) + collecting (append (list label) + (loop for n in nums collecting (cond ((equal n "NIL") 0.0) ;;bad fix! BAD! + (t (coerce (parse-decimal n) 'short-float))))))) + + + ) + + (setf *head header) + + (loop for (term . rest) in numerical-lines + do(loop for i = 1 + then (incf i) + for window in rest + do(sql:with-transaction + (sql:insert-records + :into [|numerical_data|] + :attributes '([|timecourse_data_id|] + [|term_name|] + [|window_start|] + [|window_end|] + [|data|]) + :values (list data-id + term + (first (nth i header)) + (second (nth i header)) + window) + :database (connection clh)))) + + + ) + ) + ) + +(defmethod store-numerical-and-probe-data ((clh clarity-handle) data-id file) + (let* ((lines (file-lines file)) + (split-lines (loop for line in lines + collecting (split-sequence:split-sequence #\Tab line :remove-empty-subseqs t) + )) + (head (first split-lines)) + #|header of form "term_name 0 2 TAB 2 4 TAB 4 8 + want '(term name ('(0 2) . . .'(4 8)))|# + (header (remove-if (lambda (x) + (equal x nil)) + (append (list (first head)) + (loop for nums in (rest head) + collecting (cond ((equal nums "NIL") nil) + (t (loop for dig in + (split-sequence:split-sequence #\Space nums :remove-empty-subseqs t) + collecting (cond ((equal dig nil) nil) + (t (coerce (parse-decimal dig) 'short-float)))))))))) + + (numerical-lines (loop for (label . nums) in (rest split-lines) + collecting (append (list label) + (loop for i from 0 to (- (length nums) 1) by 2 + collecting (list (cond ((equal (nth i nums) "NIL") 0.0) ;;bad fix! BAD! + (t (coerce (parse-decimal (nth i nums)) + 'short-float))) + (nth (+ i 1) nums) + ) + ))))) + + + (loop for (term . rest) in numerical-lines + do(loop for i = 1 + then (incf i) + for (window-num probes) in rest + do(sql:with-transaction + (sql:insert-records + :into [|numerical_data|] + :attributes '([|timecourse_data_id|] + [|term_name|] + [|window_start|] + [|window_end|] + [|data|] + [|probe_ids|]) + :values (list data-id + term + (first (nth i header)) + (second (nth i header)) + window-num + probes) + :database (connection clh)))) + + + ))) + + +(defun flatten (list) + (cond + ((null list) list) + ((atom list) (list list)) + (t (append (flatten (first list)) + (flatten (rest list)))))) + +(defvar store) + +(defmethod store-gantt-chart ((clh clarity-handle) data_id chart) + ;;store a single gantt chart + (let ((to-store) + (term-name (first chart)) + (string (second chart))) + (setf to-store (list data_id term-name string)) + (setf store to-store) + (sql:with-transaction + (sql:insert-records :into [|gantt_chart|] + :attributes '([|timecourse_data_id|] [|term_name|] [|sequence|]) + :values to-store + :database (connection clh) + ))) + ) + + + + + + +(defmethod lastid ((clh clarity-handle) &key table) + (cond ((equal table "timecourse_data")(first (first (sql:query + "SELECT MAX(id) FROM timecourse_data;" + :database (connection clh))))) + ((equal table "tree") (first (first (sql:query + "SELECT MAX(id) FROM tree;" + :database (connection clh))))) + + ((equal table "consensus")(first (first (sql:query + "SELECT MAX(id) FROM consensus;" + :database (connection clh))))) + ((equal table "gantt_chart") + (first (first (sql:query + "SELECT MAX(id) FROM gantt_chart;" + :database (connection clh))))) + (t 0);unknown table + )) + + +(defun file-lines (path) + "Sucks up an entire file from PATH into a list of freshly-allocated + strings, returning two values: the list of strings and the number of + lines read." + (with-open-file (s path) + (loop for line = (read-line s nil nil) + while line + collect line into lines + counting t into line-count + finally (return (values lines line-count))))) + + + +(defmethod get-children (node-id) + (let ((children + (first (sql:with-transaction + (sql:select [node_left] [node_right] + :from [|tree|] + :where [= [id] node-id] + :database (connection *current-clarity-handle*) + ))))) + (cond ((and (= (first children) 0) + (= (second children) 0)) + nil) + ((= (first children) 0) + (list (second children))) + ((= (second children) 0) + (list (first children))) + (t children)) + )) + + +(defmethod get-node-terms ((clh clarity-handle) node-id) + ;;node id is TREE id. may be either a consensus seq or real data + (if (get-children node-id) + ;;then it's a consensus + (flatten (get-consensus-terms clh node-id)) + ;;is actual data + (flatten (get-data-terms clh + (first (sql:with-transaction + (sql:select [timecourse_data_id] + :from [|tree|] + :where [= [id] node-id] + :database (connection clh) + :flatp t))))) + ) + ) + +(defmethod get-all-data ((clh clarity-handle)) + (sql:with-transaction + (sql:select [id] [datafile_path] [creation_date] + :from [|timecourse_data|] + :database (connection clh))) + ) + + +#.(sql:disable-sql-reader-syntax) + +;;; end of file -- database-functions.lisp -- Added: decimal-number.lisp ============================================================================== --- (empty file) +++ decimal-number.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,26 @@ +;;Utility from Cliki: the common lisp wiki + +;(use-package "SPLIT-SEQUENCE") + + +(in-package "CLARITY") + +(defun read-string-while (test &optional (stream *standard-input*) (eof-value nil) (recursive-p nil)) + (coerce (loop as x = (peek-char nil stream nil eof-value recursive-p) + while (and (not (equal x eof-value)) (funcall test x)) + collect (read-char stream nil eof-value recursive-p)) 'string)) + +(defun decimal-reader (s c n) (declare (ignore c n)) (parse-decimal (read-string-while #'constituentp s nil t))) + +(defun parse-decimal (str) + (let* ((parts (split-sequence::split-sequence #\. str)) + (a (car parts)) + (b (cadr parts)) + (a1 (parse-integer a)) + (b1 (or (parse-integer (or b "0") :junk-allowed t) 0))) + (+ a1 (/ b1 (expt 10 (length b)))))) + +(defun use-decimal () (set-dispatch-macro-character #\# #\D #'decimal-reader *readtable*)) + + +;;; end of file -- decimal-number.lisp -- \ No newline at end of file Added: doc/html/clarity-package.html ============================================================================== --- (empty file) +++ doc/html/clarity-package.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,124 @@ +<html> + <head> + <title>CLARITY PACKAGE</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #330066;"> + <strong><i>CLARITY PACKAGE</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="../index.html" class="navigation-link">Previous</a> + | <a href="connect.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../../../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../../../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../../../images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1><i>Package</i> <strong>CLARITY</strong></h1> + + <h2>Nicknames:</h2> + + <p>None</p> + + <h2>Uses:</h2> + + <p><code>COMMON-LISP</code></p> + + + <h2>Description:</h2> + + <p>This package contains all the symbols (and definitions) of the <strong>CLARITY</strong> library.</p> + + <h2>Affected By:</h2> + + <p>None.</p> + + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + + <h2>See Also:</h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24</strong><br> + Completed description. + </li> + + </ul> + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/clarity-schema.png ============================================================================== Binary file. No diff available. Added: doc/html/dictionary.html ============================================================================== --- (empty file) +++ doc/html/dictionary.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,174 @@ +<html> + <head> + <title>CLARITY Dictionary</title> + <link rel="stylesheet" href="style.css"> + +  + + + </head> + +<body> +<div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY Dictionary</i></strong> + <div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1>CLARITY Dictionary</h1> + + <p>The following entries are part of the <strong>CLARITY</strong> + dictionary.</p> + + + <ul> + <li><a href="dictionary/CLARITY-package.html"><i>Package</i> <b>CLARITY</b></a></li> + <li><a href="dictionary/connect.html"><i>Function</i> <b>connect</b></a></li> + <li><a href="dictionary/insert.html"><i>Function</i> <b>insert</b></a></li> + <li><a href="dictionary/ganttify.html"><i>Function</i> <b>ganttify</b></a></li> + <li><a href="dictionary/get-children.html"><i>Function</i> <b>get-children</b></a></li> + <li><a href="dictionary/get-node-terms.html"><i>Function</i> <b>get-node-terms</b></a></li> + <li><a href="dictionary/get-all-data.html"><i>Function</i> <b>get-all-data</b></a></li> + <li><a href="dictionary/store-gantt-charts.html"><i>Function</i> <b>store-gantt-charts</b></a></li> + <li><a href="dictionary/store-numerical-data.html"><i>Function</i> <b>store-numerical-data</b></a></li> + <li><a href="dictionary/store-gantt-chart.html"><i>Function</i> <b>store-gantt-chart</b></a></li> + <li><a href="dictionary/lastid.html"><i>Function</i> <b>lastid</b></a></li> + <li><a href="dictionary/.html"><i></i> <b></b></a></li> + </ul> + +  + <ul> + <li><a href="dictionary/alignment.html"><i>Standard class</i> <b>alignment</b></a></li> + <li><a href="dictionary/alignment-item.html"><i>Standard class</i> <b>alignment-item</b></a></li> + <li><a href="dictionary/align-charts.html"><i>Function</i> <b>align-charts</b></a></li> + <li><a href="dictionary/score-pair.html"><i>Function</i> <b>score-pair</b></a></li> + <li><a href="dictionary/score-pair-consensus.html"><i>Function</i> <b>score-pair-consensus</b></a></li> + <li><a href="dictionary/align-to-consensus.html"><i>Function</i> <b>align-to-consensus</b></a></li> + <li><a href="dictionary/string-alignment.html"><i>Function</i> <b>string-alignment</b></a></li> + <li><a href="dictionary/score.html"><i>Function</i> <b>score</b></a></li> + + <li><a href="dictionary/get-root.html"><i>Function</i> <b>get-root</b></a></li> + <li><a href="dictionary/tree-insert.html"><i>Function</i> <b>tree-insert</b></a></li> + <li><a href="dictionary/tree-insert-recursive.html"><i>Function</i> <b>tree-insert-recursive</b></a></li> + <li><a href="dictionary/insert-node.html"><i>Function</i> <b>insert-node</b></a></li> + <li><a href="dictionary/build-consensus.html"><i>Function</i> <b>build-consensus</b></a></li> + <li><a href="dictionary/store-consensus-sequence.html"><i>Function</i> <b>store-consensus-sequence</b></a></li> + <li><a href="dictionary/get-consensus-terms.html"><i>Function</i> <b>get-consensus-terms</b></a></li> + <li><a href="dictionary/get-data-terms.html"><i>Function</i> <b>get-data-terms</b></a></li> + </ul> + + + + + + <hr> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <a href="mailto:samantha_PROVA_A_SPAMMARME@bioinformatics.nyu.edu">me</a>. + </p> + + </div> + </div> + + + +  + + + + + + + <div class="content"> + <div class="text"> + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24</strong><br> + Page created. + </li> + </ul> + + </div> + </div> + + + + + + + + + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/align-charts.html ============================================================================== --- (empty file) +++ doc/html/dictionary/align-charts.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,157 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function ALIGN-CHARTS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function ALIGN-CHARTS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="alignment-item.html" class="navigation-link">Previous</a> + | <a href="score-pair.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>ALIGN-CHARTS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>align-charts</b> <i>cl-handle timecourse-id-1 timecourse-id-2</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>timecourse-id-1</code></i>---an <i>integer</i> + <p><i><code>timecourse-id-2</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function align-charts aligns two datasets, given their timecourse data ids. + It takes three parameters, <i>cl-handle</i>, which preserves the session; and timecourse-id-1 and timecourse-id-2, + which are the numerical ids identifying the timecourse datasets in the database. The function returns a hash table + containing alignments hashed by score.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>align-charts</b> (<i>cl-handle</i> clarity-handle) (<i>timecourse-id-1</i> integer) (<i>timecourse-id-2</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>align-charts</b> cl-handle 6 8) + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="score-pair.html">SCORE-PAIR</a><br> + <a href="score-pair-consensus.html">SCORE-PAIR-CONSENSUS</a><br> + <a href="align-to-consensus.html">ALIGN-TO-CONSENSUS</a><br> + <a href="string-alignment.html">STRING-ALIGNMENT</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/align-to-consensus.html ============================================================================== --- (empty file) +++ doc/html/dictionary/align-to-consensus.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,157 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function ALIGN-TO-CONSENSUS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function ALIGN-TO-CONSENSUS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="score-pair-consensus.html" class="navigation-link">Previous</a> + | <a href="string-alignment.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>ALIGN-TO-CONSENSUS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>align-to-consensus</b> <i>cl-handle timecourse-id consensus-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>timecourse-id</code></i>---an <i>integer</i> + <p><i><code>consensus-id</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function align-to-consensus aligns a timecourse dataset to a consensus of sequences. + It takes three parameters, <i>cl-handle</i>, which preserves the session; timecourse-id which identifies the timecourse data + and consensus id which is the numerical id identifying the consensus sequences (note that consensus id is interchangeable with + tree id in this case) in the database. The function returns a hash table containing alignments hashed by score.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>align-to-consensus</b> (<i>cl-handle</i> clarity-handle) (<i>timecourse-id</i> integer) (<i>consensus-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>align-to-consensus</b> cl-handle 6 8) + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="score-pair.html">SCORE-PAIR</a><br> + <a href="score-pair-consensus.html">SCORE-PAIR-CONSENSUS</a><br> + <a href="align-charts.html">ALIGN-CHARTS</a><br> + <a href="string-alignment.html">STRING-ALIGNMENT</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/alignment-item.html ============================================================================== --- (empty file) +++ doc/html/dictionary/alignment-item.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,135 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function ALIGNMENT-ITEM</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function ALIGNMENT-ITEM</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="alignment.html" class="navigation-link">Previous</a> + | <a href="align-charts.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Standard Class</i> <strong>ALIGNMENT-ITEM</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Class Precedence List:</h2> + + <p> alignment-item, STRUCTURE-OBJECT, T + </p> + + <h2>Slots:</h2> + <ul> + <li>DATASET-ID accessor alignment-item-dataset-id</li> + <li>CHART-ID accessor alignment-item-chart-id</li> + <li>TERM-NAME accessor alignment-item-term-name</li> + <li>STRING accessor alignment-item-string</li> + </ul> + <h2>Description:</h2> + + <p>The alignment-item structure is used to store information for terms about to be aligned. The dataset-id will be either + a timecourse dataset id or a tree node id depending on whether the the node the item belongs to is an internal (consensus) node + or a leaf node. Chart-id is the id of the item in the gantt_chart table. String is the gantt chart as created with the ganttify function.</p> + + <p>The constructor for this class is new-alignment-item. The accessors alignment-item-dataset-id, alignment-item-chart-id + alignment-item-term-name and alignment-item-string can be used to read or write their respective fields.</p> + + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="alignment.html">ALIGNMENT</a><br> + <a href="ganttify.html">GANTTIFY</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/alignment.html ============================================================================== --- (empty file) +++ doc/html/dictionary/alignment.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,129 @@ +<html> + <head> + <title>CLARITY: Standard Class ALIGNMENT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Class ALIGNMENT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="lastid.html" class="navigation-link">Previous</a> + | <a href="alignment-item.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Standard Class</i> <strong>ALIGNMENT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Class Precedence List:</h2> + + <p> ALIGNMENT, STRUCTURE-OBJECT, T + </p> + + <h2>Slots:</h2> + <ul> + <li>SCORE accessor alignment-score</li> + <li>ITEMS accessor alignment-items</li> + </ul> + <h2>Description:</h2> + + <p>The alignment class stores pairs of instances of the alignment-item class as well as the score of the aligned items. + The constructor for this class is new-alignment. The accessors alignment-score and alignment items can be used to read or write + their respective fields.</p> + + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="alignment-item.html">ALIGNMENT-ITEM</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/build-consensus.html ============================================================================== --- (empty file) +++ doc/html/dictionary/build-consensus.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,152 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function BUILD-CONSENSUS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function BUILD-CONSENSUS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="insert-node.html" class="navigation-link">Previous</a> + | <a href="store-consensus-sequence.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>BUILD-CONSENSUS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>build-consensus</b> <i>cl-handle data-left data-right</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>data-left</code></i>---an <i>integer</i> + <p><i><code>data-right</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function build-consensus takes two nodes, computes their consensus sequence, and then stores it in the database. + It takes three parameters, clarity-handle, which identifies the clarity database; data-left, which may be either a timecourse_id + or a consensus id and sdata-right, which is a timecourse id.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>build-consensus</b> (<i>cl-handle</i> clarity-handle) (<i>data-left</i> integer) (<i>data-right</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>build-consensus</b> cl-handle 7 9)</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/connect.html ============================================================================== --- (empty file) +++ doc/html/dictionary/connect.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,173 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function CONNECT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function CONNECT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="clarity-package.html" class="navigation-link">Previous</a> + | <a href="insert.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>CONNECT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>connect</b> <i>db-spec</i> + => <i>database-connection</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>db spec</code></i>---a <i>string</i> + <p><i><code>(optional) connection</code></i>--- a <i>string</i> + + + <h2>Description:</h2> + + <p>The generic function connect sets up a connection to an underlying CLARITY database for the handle. + It takes two parameter, <i>clarity handle</i>, to preserve one's session, and <i>db-spec</i> + a database connection string. </p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>connect</b> (<i>clarity-handle-object</i> clarity-handle) (<i>dp-spec</i> string) + => <i>database-connection</i> + </pre> + </p> + + <p></p> + </li> + + <li> + <p> + <pre> + <b>connect</b> (<i>clarity-handle-object</i> clarity-handle) (<i>dp-spec</i> string)) + => <i>database-connection</i> + </pre> + </p> + + <p>This uses the method sqlcon in place of a connection string.&nbsp In this case, db spec would be the null + string, "".</p> + </li> + + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>connect</b> myclarityhandle "data source name/user/password") +#<CLARITY:CLARITY-HANDLE 2061155C> connecting as "data source name/user" +#<SQL::ODBC-DATABASE "data source name/user" 205F450C></pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/ganttify.html ============================================================================== --- (empty file) +++ doc/html/dictionary/ganttify.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,158 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GANTTIFY</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GANTTIFY</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="connect.html" class="navigation-link">Previous</a> + | <a href="get-children.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GANTTIFY</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>ganttify</b> <i>clarity-handle filename filedate</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>clarity handle</code></i>---a <i>clarity-handle</i> + <p><i><code>filename</code></i>--- a <i>string</i> or <i>path</i> + <p><i><code>filedate</code></i>--- a <i>string</i> + + + <h2>Description:</h2> + + <p>The generic function ganttify ganttifys a datafile into the database. It calls the functions ganttify, store-gantt-charts as well as store-numerical-data. + The function then pops up a confirmer, where a user may select to add the data to the tree. + It takes three parameters, <i>clarity handle</i>, to preserve one's session, <i>filename</i> + the location of the data to be ganttifyed and <i>filedate</i> the creation date of the file. </p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>ganttify</b> (<i>clarity-handle-object</i> clarity-handle) (<i>filename</i> string) (<i>filedate</i> string) + </pre> + </p> + + <p></p> + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>ganttify</b> myclarityhandle "C:/Files/myfile.txt" "MO/DAY/YR")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-all-data.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-all-data.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,150 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-ALL-DATA</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-ALL-DATA</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="get-node-terms.html" class="navigation-link">Previous</a> + | <a href="store-gantt-charts.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-ALL-DATA</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-all-data</b> <i>cl-handle</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + + <h2>Description:</h2> + + <p>The generic function get-all-data gets all of the rows in the timecourse data table of the database. + It takes one parameter, <i>cl-handle</i>, which preserves the session and identifies the database.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-all-data</b> (<i>cl-handle</i> clarity-handle) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-all-data</b> cl-handle) +</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-children.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-children.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,152 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-CHILDREN</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-CHILDREN</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="ganttify.html" class="navigation-link">Previous</a> + | <a href="get-node-terms.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-CHILDREN</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-children</b> <i>node-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>node-id</code></i>---an <i>integer</i> + + + <h2>Description:</h2> + + <p>The generic function get-children gets left and right child of node in a phylogenetic tree. + It takes one parameter, <i>node-id</i>, the unique identifier of the node in the tree and returns the + ids of the nodes two children, or nil if it is a leaf node. </p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-children</b> (<i>node-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-children</b> 6) +cl-prompt: (8 12)</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-consensus-terms.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-consensus-terms.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,155 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-CONSENSUS-TERMS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-CONSENSUS-TERMS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="store-consensus-sequence.html" class="navigation-link">Previous</a> + | <a href="get-data-terms.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-CONSENSUS-TERMS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-consensus-terms</b> <i>cl-handle node-id term-name sequence</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>node-id</code></i>---an <i>integer</i> + + + <h2>Description:</h2> + + <p>The generic function get-consensus-terms gets the corresponding consensus terms from the database for a + node in the tree. It takes two parameters, clarity-handle, which identifies the clarity database; and node-id, the + integer id of the tree node for which to find the terms. It returns a list of the ontology terms that are in the + consensus.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-consensus-terms</b> (<i>cl-handle</i> clarity-handle) (<i>node-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-consensus-terms</b> cl-handle 7) +cl-prompt: '("Apoptosis" "M phase of mitotic cell cycle" "pathogenesis")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2><a href="build-consensus.html">BUILD-CONSENSUS</a><br> + <a href="get-consensus-terms.html">GET-CONSENSUS-TERMS</a></h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-data-terms.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-data-terms.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,154 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-DATA-TERMS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-DATA-TERMS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="get-consensus-terms.html" class="navigation-link">Previous</a> + | <a href="../dictionary.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-DATA-TERMS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-data-terms</b> <i>cl-handle node-id term-name sequence</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>data-id</code></i>---an <i>integer</i> + + + <h2>Description:</h2> + + <p>The generic function get-data-terms gets the corresponding consensus terms from the database for a + node in the tree. It takes two parameters, clarity-handle, which identifies the clarity database; and data-id, the + integer id of the timecourse dataset for which to find the terms. It returns a list of the ontology terms that are in the + consensus.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-data-terms</b> (<i>cl-handle</i> clarity-handle) (<i>data-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-data-terms</b> cl-handle 9) +cl-prompt: '("Apoptosis" "M phase of mitotic cell cycle" "pathogenesis")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>None.</h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-29 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-node-terms.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-node-terms.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,152 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-NODE-TERMS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-NODE-TERMS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="get-children.html" class="navigation-link">Previous</a> + | <a href="get-all-data.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-NODE-TERMS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-node-terms</b> <i>node-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>node-id</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function get-node-terms gets all of the terms associated with a tree node in the phylogenetic tree. + It takes one parameter, <i>node-id</i>, the unique identifier of the node in the tree and returns the + terms associated with the node. These terms will be part of the dataset associated with the node if it is a leaf + or part of the consensus sequence associated with the node if it is internal.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-node-terms</b> (<i>node-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-node-terms</b> 6) +cl-prompt: ("cell death" "M phase" "mitotic anaphase A")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/get-root.html ============================================================================== --- (empty file) +++ doc/html/dictionary/get-root.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,150 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function GET-ROOT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function GET-ROOT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="score.html" class="navigation-link">Previous</a> + | <a href="tree-insert.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>GET-ROOT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>get-root</b> <i>cl-handle</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + + <h2>Description:</h2> + + <p>The generic function get-root returns the tree id of the root node in the phylogenetic tree. It takes one parameter, + clarity-handle, which identifies the clarity database.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>get-root</b> (<i>cl-handle</i> clarity-handle) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>get-root</b> cl-handle) +cl-prompt: 8</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/insert-node.html ============================================================================== --- (empty file) +++ doc/html/dictionary/insert-node.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,154 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function INSERT-NODE</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function INSERT-NODE</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="tree-insert.html" class="navigation-link">Previous</a> + | <a href="build-consensus.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>INSERT-NODE</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>insert-node</b> <i>cl-handle new-node-id sibling-node-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>new-node-id</code></i>---an <i>integer</i> + <p><i><code>sibling-node-id</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function insert-node inserts a new node as the sibling of the specified node in the phylogenetic tree. + It creates a parent node for the specified nodes and inserts it in the appropriate place. The function takes three parameters, + clarity-handle, which identifies the clarity database; new-node, which is the integer id of the new node in the tree table + of the database and sibling-node-id, which is the id of the node to which the new node is most similar and the node + which will be its sibling in the phylogenetic tree.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>insert-node</b> (<i>cl-handle</i> clarity-handle) (<i>new-node-id</i> integer) (<i>sibling-node-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>insert-node</b> cl-handle 7 9)</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/insert.html ============================================================================== --- (empty file) +++ doc/html/dictionary/insert.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,158 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function INSERT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function INSERT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="connect.html" class="navigation-link">Previous</a> + | <a href="ganttify.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>INSERT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>insert</b> <i>clarity-handle filename filedate</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>clarity handle</code></i>---a <i>clarity-handle</i> + <p><i><code>filename</code></i>--- a <i>string</i> or <i>path</i> + <p><i><code>filedate</code></i>--- a <i>string</i> + + + <h2>Description:</h2> + + <p>The generic function insert inserts a datafile into the database. It calls the functions ganttify, store-gantt-charts as well as store-numerical-data. + The function then pops up a confirmer, where a user may select to add the data to the tree. + It takes three parameters, <i>clarity handle</i>, to preserve one's session, <i>filename</i> + the location of the data to be inserted and <i>filedate</i> the creation date of the file. </p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>insert</b> (<i>clarity-handle-object</i> clarity-handle) (<i>filename</i> string) (<i>filedate</i> string) + </pre> + </p> + + <p></p> + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>insert</b> myclarityhandle "C:/Files/myfile.txt" "MO/DAY/YR")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/lastid.html ============================================================================== --- (empty file) +++ doc/html/dictionary/lastid.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,152 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function LASTID</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function LASTID</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="store-gantt-chart.html" class="navigation-link">Previous</a> + | <a href="alignment.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>LASTID</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>lastid</b> <i>cl-handle table</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>table</code></i>---a <i>string</i> + + <h2>Description:</h2> + + <p>The generic function lastid returns the value of the more recently created id number for a table. + It takes two parameters, <i>cl-handle</i>, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and <i>table</i> a string that identifies the table.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>lastid</b> (<i>cl-handle</i> clarity-handle) (<i>table</i> string) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>lastid</b> cl-handle :table "timecourse_data") + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/needleman-wunsch.html ============================================================================== --- (empty file) +++ doc/html/dictionary/needleman-wunsch.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,154 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function NEEDLEMAN-WUNSCH</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function NEEDLEMAN-WUNSCH</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="align-to-consensus.html" class="navigation-link">Previous</a> + | <a href="score.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>NEEDLEMAN-WUNSCH</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>needleman-wunsch</b> <i>string-1 string-2</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>string-1</code></i>---a <i>string</i> + <p><i><code>string-2</code></i>---a <i>string</i> + + <h2>Description:</h2> + + <p>The generic function needleman-wunsch uses the Needleman Wunsch algorithm to align two strings and then returns their + alignment score. It takes two parameters <i>string-1<i> and <i>string-2</i>, the strings to be aligned.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>needleman-wunsch</b> (<i>string-1</i> string) (<i>string-2</i> string) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>needleman-wunsch</b> "UDUUID" "UUDDID") + cl-prompt: -2</pre></p> + + <h2>Affected By:</h2> + + <p><a href="score.html">SCORE</a></p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="score-pair.html">SCORE-PAIR</a><br> + <a href="score-pair-consensus.html">SCORE-PAIR-CONSENSUS</a><br> + <a href="align-charts.html">ALIGN-CHARTS</a><br> + <a href="align-to-consensus.html">ALIGN-TO-CONSENSUS</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/score-pair-consensus.html ============================================================================== --- (empty file) +++ doc/html/dictionary/score-pair-consensus.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,157 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function SCORE-PAIR-CONSENSUS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function SCORE-PAIR-CONSENSUS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="align-charts.html" class="navigation-link">Previous</a> + | <a href="align-to-consensus.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>SCORE-PAIR-CONSENSUS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>score-pair-consensus</b> <i>cl-handle timecourse-id consensus-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>timecourse-id</code></i>---an <i>integer</i> + <p><i><code>consensus-id</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>Given a time course id and a consensus id (note that the consensus id is equivalent to a tree id), + score-pair-consensus computes their alignment and returns the score. + It takes three parameters, <i>cl-handle</i>, which preserves the session; timecourse-id which identifies the timecourse + dataset and consensus id which identifies the consensus sequence in the database.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>score-pair-consensus</b> (<i>cl-handle</i> clarity-handle) (<i>timecourse-id</i> integer) (<i>consensus-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>score-pair-consensus</b> cl-handle 6 8) + cl-prompt: 12</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="align-charts.html">ALIGN-CHARTS</a><br> + <a href="score-pair.html">SCORE-PAIR</a><br> + <a href="align-to-consensus.html">ALIGN-TO-CONSENSUS</a><br> + <a href="string-alignment.html">STRING-ALIGNMENT</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/score-pair.html ============================================================================== --- (empty file) +++ doc/html/dictionary/score-pair.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,156 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function SCORE-PAIR</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function SCORE-PAIR</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="align-charts.html" class="navigation-link">Previous</a> + | <a href="score-pair-consensus.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>SCORE-PAIR</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>score-pair</b> <i>cl-handle timecourse-id-1 timecourse-id-2</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>timecourse-id-1</code></i>---an <i>integer</i> + <p><i><code>timecourse-id-2</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>Given two timecourse data ids, score-pair computes their alignment and returns the score. + It takes three parameters, <i>cl-handle</i>, which preserves the session; and timecourse-id-1 and timecourse-id-2, + which are the numerical ids identifying the timecourse datasets in the database.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>score-pair</b> (<i>cl-handle</i> clarity-handle) (<i>timecourse-id-1</i> integer) (<i>timecourse-id-2</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>score-pair</b> cl-handle 6 8) + cl-prompt: 12</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="align-charts.html">ALIGN-CHARTS</a><br> + <a href="score-pair-consensus.html">SCORE-PAIR-CONSENSUS</a><br> + <a href="align-to-consensus.html">ALIGN-TO-CONSENSUS</a><br> + <a href="string-alignment.html">STRING-ALIGNMENT</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/score.html ============================================================================== --- (empty file) +++ doc/html/dictionary/score.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,151 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function SCORE</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function SCORE</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="align-to-consensus.html" class="navigation-link">Previous</a> + | <a href="get-root.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>SCORE</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>score</b> <i>char1 char2</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>char-1</code></i>---a <i>character</i> + <p><i><code>char-2</code></i>---a <i>character</i> + + <h2>Description:</h2> + + <p>The generic function score is used to compute the score of two characters during alignment using the string-alignment + function. It takes two parameters <i>char-1</i> and <i>char-2</i>, the characters being scored.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>score</b> (<i>char-1</i> character) (<i>char-2</i> character) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>score</b> #\D #\I) +cl-prompt: -1</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="string-alignment.html">STRING-ALIGNMENT</a></p> + + <h2>Notes:</h2> + + <p>This is the function that should be edited if you would like to alter the scoring.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/store-consensus-sequence.html ============================================================================== --- (empty file) +++ doc/html/dictionary/store-consensus-sequence.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,158 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function STORE-CONSENSUS-SEQUENCE</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function STORE-CONSENSUS-SEQUENCE</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="build-consensus.html" class="navigation-link">Previous</a> + | <a href="get-consensus-terms.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>STORE-CONSENSUS-SEQUENCE</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>store-consensus-sequence</b> <i>cl-handle node-id term-name sequence</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>node-id</code></i>---an <i>integer</i> + <p><i><code>term-name</code></i>---a <i>string</i> + <p><i><code>sequence</code></i>---a <i>string</i> + + + <h2>Description:</h2> + + <p>The generic function store-consensus-sequence stores a consensus sequence and its identifying information + in the database. It takes four parameters, clarity-handle, which identifies the clarity database; node-id, the + integer id of the tree node the consensus sequence belongs to; term name, and sequence which is a gantt chart + sequence.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>store-consensus-sequence</b> (<i>cl-handle</i> clarity-handle) (<i>node-id</i> integer) (<i>term-name</i> string) + (<i>sequence</i> string) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>store-consensus-sequence</b> cl-handle 7 "apoptosis" "UDDIDN")</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2><a href="ganttify.html">GANTTIFY</a><br> + <a href="build-consensus.html">BUILD-CONSENSUS</a><br> + <a href="get-consensus-terms.html">GET-CONSENSUS-TERMS</a></h2> + + <p>None.</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/store-gantt-chart.html ============================================================================== --- (empty file) +++ doc/html/dictionary/store-gantt-chart.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,153 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function STORE-GANTT-CHART</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function STORE-GANTT-CHART</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="store-numerical-data.html" class="navigation-link">Previous</a> + | <a href="lastid.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>STORE-GANTT-CHART</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>store-gantt-chart</b> <i>cl-handle data-id file</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>data-id</code></i>---an <i>integer</i> + <p><i><code>chart</code></i>---a <i>list</i> + + <h2>Description:</h2> + + <p>The generic function store-gantt-chart stores a single gantt chart and term associated with a dataset in the database. + It takes three parameters, <i>cl-handle</i>, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a list of the term and its associated gantt chart.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>store-gantt-chart</b> (<i>cl-handle</i> clarity-handle) (<i>data-id</i> integer) (<i>chart</i> list) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>store-gantt-chart</b> cl-handle 6 '("apoptosis" "UUDDUUNN")) + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/store-gantt-charts.html ============================================================================== --- (empty file) +++ doc/html/dictionary/store-gantt-charts.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,153 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function STORE-GANTT-CHARTS</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function STORE-GANTT-CHARTS</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="get-all-data.html" class="navigation-link">Previous</a> + | <a href="store-numerical-data.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>STORE-GANTT-CHARTS</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>store-gantt-charts</b> <i>cl-handle data-id chart-list</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>data-id</code></i>---an <i>integer</i> + <p><i><code>chart-list</code></i>---a <i>list</i> + + <h2>Description:</h2> + + <p>The generic function store-gantt-charts takes a list of gantt charts and stores them in the database. + It takes three parameters, <i>cl-handle</i>, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a list of gantt charts created with the ganttify function.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>store-gantt-charts</b> (<i>cl-handle</i> clarity-handle) (<i>data-id</i> integer) (<i>chart-list</i> list) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>store-gantt-charts</b> cl-handle 6 '(("cell cycle" "UDUDU") ("apoptosis" "DDUUU"))) + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="ganttify.html">GANTTIFY</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/store-numerical-data.html ============================================================================== --- (empty file) +++ doc/html/dictionary/store-numerical-data.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,153 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function STORE-NUMERICAL-DATA</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function STORE-NUMERICAL-DATA</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="store-gantt-charts.html" class="navigation-link">Previous</a> + | <a href="store-gantt-chart.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>STORE-NUMERICAL-DATA</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>store-numerical-data</b> <i>cl-handle data-id file</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>cl-handle</i> + <p><i><code>data-id</code></i>---an <i>integer</i> + <p><i><code>file</code></i>---a <i>path</i> to a file + + <h2>Description:</h2> + + <p>The generic function store-numerical-data takes a file containing a numerical timecourse dataset and stores it in the database. + It takes three parameters, <i>cl-handle</i>, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a path to the file to insert.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>store-numerical-data</b> (<i>cl-handle</i> clarity-handle) (<i>data-id</i> integer) (<i>file</i> path) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>store-numerical-data</b> cl-handle 6 "C:/data/dataset.txt") + </pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p>None</p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/string-alignment.html ============================================================================== --- (empty file) +++ doc/html/dictionary/string-alignment.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,154 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function STRING-ALIGNMENT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function STRING-ALIGNMENT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="align-to-consensus.html" class="navigation-link">Previous</a> + | <a href="score.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>STRING-ALIGNMENT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>string-alignment</b> <i>string-1 string-2</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>string-1</code></i>---a <i>string</i> + <p><i><code>string-2</code></i>---a <i>string</i> + + <h2>Description:</h2> + + <p>The generic function string-alignment uses a variant of the Needleman-Wunsch and Smith-Waterman algorithms to align two strings and then returns their + alignment score. It takes two parameters <i>string-1<i> and <i>string-2</i>, the strings to be aligned.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>string-alignment</b> (<i>string-1</i> string) (<i>string-2</i> string) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>string-alignment</b> "UDUUID" "UUDDID") + cl-prompt: -2</pre></p> + + <h2>Affected By:</h2> + + <p><a href="score.html">SCORE</a></p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="score-pair.html">SCORE-PAIR</a><br> + <a href="score-pair-consensus.html">SCORE-PAIR-CONSENSUS</a><br> + <a href="align-charts.html">ALIGN-CHARTS</a><br> + <a href="align-to-consensus.html">ALIGN-TO-CONSENSUS</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/tree-insert-recursive.html ============================================================================== --- (empty file) +++ doc/html/dictionary/tree-insert-recursive.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,154 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function TREE-INSERT-RECURSIVE</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function TREE-INSERT-RECURSIVE</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="tree-insert.html" class="navigation-link">Previous</a> + | <a href="insert-node.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>TREE-INSERT-RECURSIVE</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>tree-insert-recursive</b> <i>cl-handle new-node current-node</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>new-node</code></i>---an <i>integer</i> + <p><i><code>current-node</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function tree-insert-recursive inserts new data into the phylogenetic tree. It takes three parameters, + clarity-handle, which identifies the clarity database; new-node, which is the integer id of the new node in the tree table + of the database and current-node, which is the id of the current node to which the new node is being aligned. It returns two + values, the number of the node to which the alignment score was highest, as well as that score.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>tree-insert-recursive</b> (<i>cl-handle</i> clarity-handle) (<i>new-node</i> integer) (<i>current-node</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>tree-insert-recursive</b> cl-handle 7 9) + cl-prompt: 7 42</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="tree-insert.html">TREE-INSERT</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/dictionary/tree-insert.html ============================================================================== --- (empty file) +++ doc/html/dictionary/tree-insert.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,151 @@ +<html> + <head> + <title>CLARITY: Standard Generic Function TREE-INSERT</title> + <link rel="stylesheet" href="../style.css"> +  + + </head> + + <body><div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY: Standard Generic Function TREE-INSERT</title></i></strong> + <div class="navigation"> + <a href="../index.html" class="navigation-link">Home</a> + | <a href="get-root.html" class="navigation-link">Previous</a> + | <a href="tree-insert-recursive.html" class="navigation-link">Next</a> + | <a href="../downloads.html" class="navigation-link">Downloads</a> + | <a href="../links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="../images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="../images/shim.gif" height="1" width="1"></div> + </div> + + + + <div class="content"> + <div class="text"> + + <h1><i>Generic function</i> <strong>TREE-INSERT</strong></h1> + + <h2>Package:</h2> + + <p><code>CLARITY</code></p> + + <h2>Syntax:</h2> + + <p> + <pre> + <b>tree-insert</b> <i>cl-handle timecourse-data-id</i> + </pre> + </p> + + <h3>Arguments and Values:</h3> + + <p><i><code>cl-handle</code></i>---a <i>clarity-handle</i> + <p><i><code>timecourse-data-id</code></i>---an <i>integer</i> + + <h2>Description:</h2> + + <p>The generic function tree-insert inserts new data into the phylogenetic tree. It takes two parameters, + clarity-handle, which identifies the clarity database; and timecourse-data-id, the id of the new data to be inserted. + It calls the recursive function tree-insert-recursive after creating a new tree node for the data.</p> + + + <h3><a name="known_methods">Known Methods</a>:</h3> + + <p> + <ul> + <li> + <p> + <pre> + <b>tree-insert</b> (<i>cl-handle</i> clarity-handle) (<i>timecourse-data-id</i> integer) + </pre> + </p> + + </li> + </ul> + </p> + + <h2>Examples:</h2> + + <p><pre>cl-prompt: (clarity:<b>tree-insert</b> cl-handle 7)</pre></p> + + <h2>Affected By:</h2> + + <p>None.</p> + + <h2>Exceptional Situations:</h2> + + <p>None.</p> + + <h2>See Also:</h2> + + <p><a href="tree-insert-recursive.html">TREE-INSERT-RECURSIVE</a></p> + + <h2>Notes:</h2> + + <p>None.</p> + + + + <hr> + + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-26 </strong><br> + Completed description. + </li> + + </ul> + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/downloads.html ============================================================================== --- (empty file) +++ doc/html/downloads.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,157 @@ +<html> + <head> + <title>CLARITY Download Page</title> + <link rel="stylesheet" href="style.css"> + +  + + + </head> + +<body> +<div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY</i></strong> + <div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + </div> + + + + + + + <div class="content"> + <div class="text"> + + <h1>CLARITY Download Page</h1> + + <hr> + <em> + <p> + <b>DISCLAIMER:</b> The code associated to these documents is not + completely tested and it is bound to contain errors and omissions. + This documentation may contain errors and omissions as well.</p> + + <p>The file <tt>COPYING</tt> contains an LGPL license. You + are advised to use the code at your own risk. No warranty + whatsoever is provided, the author will not be held responsible for + any effect generated by your use of the library, and you can put + here the scarier extra disclaimer you can think of. + </p> + </em> + <hr> + + + <h2>Download and CVS Repository</h2> + + <p>The CVS repository is <a href="http://common-lisp.net/cgi-bin/viewcvs.cgi/?root=clarity">here</a>. + You can download a tarball directly from there.</p> + + + + + + + <hr> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <a href="mailto:samantha_PROVA_A_SPAMMARME@bioinformatics.nyu.edu">me</a>. + </p> + + </div> + </div> + + + +  + + + + + + + <div class="content"> + <div class="text"> + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-07-24</strong><br> + Page created. + </li> + </ul> + + </div> + </div> + + + + + + + + + + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + + + </div></body> +</html> Added: doc/html/gui.html ============================================================================== --- (empty file) +++ doc/html/gui.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,129 @@ +<!DOCTYPE html +PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html> + <head> + <title>CLARITY GUI</title> + <link rel="stylesheet" href="style.css"/> + + + +  + + + + </head> + + <body> + <div id="main"> + <div class="header"> + <strong><i>CLARITY GUI</i></strong><div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a></div> + + <div class="black-line"> + <img src="images/shim.gif" height="1" width="1" alt="placeholder"/></div> + <div class="middle-bar" + <img src="images/shim.gif" height="5" width="1" alt="placeholder"/></div> + <div class="black-line"> + <img src="images/shim.gif" height="1" width="1" alt="placeholder"/></div> + + </div> + + + + + <div class="content"> + + <div class="text"> + + <h1>CLARITY GUI</h1> + + <h2>About the GUI</h2> + + <p>The CLARITY GUI allows users to insert data into the databse, browse the database, and view the phylogenetic-like tree. + Users may view similarities between datasets at various levels of resolution. + </p> + <p>CL-GODB Screenshot </p> + <p><img src="images/phylogeny-3.jpg" alt="Screenshot of the CLARITY GUI"></p> + <h2>Interface Overview</h2> + + + <h3>1. Phylogenetic Tree View</h3> + <p>The area below the "Phylogeny" tab is where the tree of data is displayed. A 0 indicates an internal node, which contains a collection of + consensus terms. Nodes with numerical values are labelled with the id number of the dataset with which they are associated. Clicking on an + internal node will display information in regions 2 and 3 of the above diagram. Clicking on a leaf node will display information in the leaf + node tab, which can be selected by clicking.</p> + <h3>2. Left and Right Information</h3> + <p>These panels, displayed as tree views, contain the terms that are either not in the intersection of the two children of the selected node, + or those which are regulated differently. Clicking on each term in these panels will expand the tree and display a number of windows with colored + icons. The icons represent the terms overall regulation, or activity, in that window of time. Green denotes a term which is down regulated, + red denotes up regulation, and yellow denotes neither. If there is a plus sign next to the window's icon, it means that probe, or gene, information + was provided with the data. Clicking on these icons displays the list of genes. </p> + <h3>3. Consensus Information</h3> + <p>Selecting an internal node fills this list panel. It contains the highly similarly regulated terms of the selected node's two + immediate children.</p> + + + + <hr/> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <A href="javascript:main.compose('new','t=samantha_NO_SPAM_(a)_REMOVE_ME_bioinformatics.nyu.edu')">me</a>. + </p> + + + <a name="news"></a><br/><br/><h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-08-16</strong><br/> + Updated description. + </li> + </ul> + + </div> + </div> + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + +</div> + + +</body> +</html> \ No newline at end of file Added: doc/html/images/Thumbs.db ============================================================================== Binary file. No diff available. Added: doc/html/images/interface2.jpg ============================================================================== Binary file. No diff available. Added: doc/html/images/phylogeny-1-smaller.jpg ============================================================================== Binary file. No diff available. 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Added: doc/html/index.html ============================================================================== --- (empty file) +++ doc/html/index.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,164 @@ +<!DOCTYPE html +PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html> + <head> + <title>CLARITY</title> + <link rel="stylesheet" href="style.css"/> + + + +  + + + + </head> + + <body> + <div id="main"> + <div class="header"> + <strong><i>CLARITY</i></strong><div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a></div> + + <div class="black-line"> + <img src="images/shim.gif" height="1" width="1" alt="placeholder"/></div> + <div class="middle-bar" + <img src="images/shim.gif" height="5" width="1" alt="placeholder"/></div> + <div class="black-line"> + <img src="images/shim.gif" height="1" width="1" alt="placeholder"/></div> + + </div> + + + + + <div id="menu"> + <p> + <a href="#features" class="menu-link">Features</a><br> + <a href="#example" class="menu-link">Example Use</a><br> + <a href="#dictionary" class="menu-link">Dictionary</a><br> + <a href="#acknowledgments" class="menu-link">Acknowledgments</a><br> + <a href="#sitemap" class="menu-link">Site Map</a><br> + <a href="#news" class="menu-link">News</a><br> + </p> + </div> + + <div class="content"> + + + + <div class="text"> + + <h1>CLARITY: A Common Lisp Data Alignment Repository</h1> + + + <p>CLARITY is a tool and method for the storage and comparison of data with numeric and + set membership components.  It is specifically geared toward timecourse microarray data, which is used to + study the activity of genes across time. By using data that has been redescribed into Gene Ontology (GO) terms, and summarizing the regulation + of these terms across time using characters (together forming sequences) we are able to use standard DNA alignment techniques with + these sequences. Due to the prevalence and size of microarray experiments, finding a way to analyze new experiments as well as consider their relation + to prior work is a significant contribution. CLARITY aims to help researchers update their prior findings as new data becomes available, and + to automate this process. Contained in the software is a novel method of comparison, based on Gantt charts, which allows us to reason about + numerical data in a way that we do DNA sequences. I.e. Rather than just looking at the numbers describing one gene across time as compared to another, + we can consider insertions, deletions, mutations in these sequences of numbers. This is done efficiently using a global alignment + with an affine (linear) gap score, a variant of the Needleman-Wunsch and Smith-Waterman algorithms + + + <p> + The Gene Ontology (GO), is a controlled vocabulary used to aid the description of genes and gene product attributes in a variety of + organisms. There are three different ontologies that describe molecular functions, biological processes, and cellular components.</p> + + <a name="features"></a><br><br><h2>Features</h2> + <p><b>CLARITY</b> provides novel methods for computing and visualizing the relationship among large amounts of data. The graphical + interface allows the user to browse the database contents in text form as well as see the data arranged into a phylogenetic tree. + + There is more information on this interface <a href="gui.html">here</a> + <p><img src="images/phylogeny-2-smaller.jpg" alt="Screenshot of the phylogeny interface"> + </p> + + <a name="dictionary"></a> <br><br><h2>The CLARITY Dictionary</h2> + + <p>The <a href="dictionary.html"><strong>CLARITY</strong> + dictionary</a> contains all the definitions comprising the library. + + + <a name="acknowledgments"></a><br><br><h2>Acknowledgments</h2> + + <p>This project was sponsored by the <a + href="http://www.google.com">Google</a> <a + href="http://code.google.com/soc/">Summer of Code</a> + program. The <a href="http://www.lispnyc.org">Lisp NYC</a> group + provided moral guidance and support. The <a + href="http://bioinformatics.nyu.edu">NYU Courant + Bioinformatics Group</a> provided all the rest.</p> + + + <a name="sitemap"></a><br><br><h2>Site Map</h2> + + + <p>None yet.</p> + + + + <hr/> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <A href="javascript:main.compose('new','t=samantha_NO_SPAM_(a)_REMOVE_ME_bioinformatics.nyu.edu')">me</a>. + </p> + + + <a name="news"></a><br/><br/><h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-06-9</strong><br/> + Started the site. + </li> + </ul> + + </div> + </div> + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + +</div> + + +</body> +</html> \ No newline at end of file Added: doc/html/installation.html ============================================================================== --- (empty file) +++ doc/html/installation.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,234 @@ +<html> + <head> + <title>CLARITY Installation</title> + <link rel="stylesheet" href="style.css"> + +  + + + </head> + +<body> +<div id="main"> + + + + + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY Installation</i></strong> + <div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + </div> + + + <div id="menu"> + <p> + <a href="#requirements" class="menu-link">Requirements</a><br> + <a href="#steps" class="menu-link">Installation Steps</a><br> + <a href="#windows" class="menu-link">ClARITY for Windows</a><br> + <a href="#unix" class="menu-link">CLARITY for Unix</a><br> + <a href="#mac" class="menu-link">CLARITY for Mac</a><br> + <a href="#installclarity" class="menu-link">Load and Compile CLARITY</a><br> + <a href="#gettingstarted" class="menu-link">Getting Started</a><br> + <a href="#standalone" class="menu-link">Standalone version</a><br> + <a href="#future" class="menu-link">Future Releases</a><br> + </p> + </div> + + + <div class="content"> + <div class="text"> + + <h1>Installing the CLARITY library</h1> + + <a name="requirements"></a><br><br><h3>Requirements</h3> + <p>-MySQL<br> + -Lispworks<br> + -Common SQL + + <a name="steps"></a><br><br><h3>Installation Steps</h3> + <p>If you don't have mySQL installed, go to the <a href="http://dev.mysql.com/downloads/">MySQL Downloads</a> + page and follow their instructions. (Note: you probably want the "Community Edition - Generally Available (GA) Release") + + + + <a name="windows"></a><br><br><h4>Install CLARITY for Windows:</h4> + <p>Open the mysql command line interface (this can be done in Cygwin). Enter the root password +that was created during mysql installation. Replace the uppercase +"DATABASE" with the name of your choice, after entering the comand you will have created a database +named clarity with the tables needed for the library.</p> + <pre>mysql> \. C:/Path-to-clarity/utilities/clarity.sql;</pre> + <p>Alternatively, you may enter your password and run the creation script in one step:</p> + <pre>Prompt: mysql -u root -p < C:/Path-to-clarity/utilities/clarity.sql;</pre> +<p> +The clarity database is now set up and currently empty. +</p> +<p>You may close the command line now. Open Microsoft ODBC +Administrator (may be called "Data Sources (ODBC)" in shorcuts). +Click add and then create a new data source using the MySQL ODBC +driver. Choose a name for your Data Source (note: you will be using +this name later +when you connect with clarity), then input the User/Password you +will be using to connect to the database. If the database is on your +computer, you +you can type in "localhost" or leave the server field blank. Now you +should be able to select the database you created earlier in the drop +down menu. + + + <a name="unix"></a><br><br><h4>Install CLARITY For Unix:</h4> + <p>Coming Soon! + + <a name="mac"></a><br><br><h4>Install CLARITY For Mac: </h4> + <p>Coming soon! + + <a name="installclarity"></a><br><br><h3>Load and Compile CLARITY</h3> + <p> + Get the CLARITY tarball from the <a href="downloads.html">downloads page</a> and unpack it + into a directory where Lispworks will be able to see it. + </p> + <p> +You can either use mk:defsystem or compile and load the files in the +following order: clarity-package, decimal-number, database-functions, alignment-functions. In order to +use the gui, go into +gui/impl-dependent/lwcapi and then compile and load the insert-data-interface, clarity-interface, +clarity-interface-functions, clarity-database-setup-interface, and start-gui.</p> + <h4>Using MK:DEFSYSTEM</h4> + <p>If you don't already have it, you can download it from the <a href="http://sourceforge.net/projects/clocc">CLOCC Sourceforge page</a> + You can load it as below at the lisp prompt, or you can add that line to your Lisp startup file.</p> +<pre>cl-prompt: (load "path/to/defsystem.lisp") +; Loading text file Z:\lisp\defsystem-3.x\defsystem.lisp +#P"Z:/lisp/defsystem-3.x/defsystem.lisp"</pre> + +<p> +If you're not working in the directory where you put the CLARITY +library, you will need to add that path to your registry. Otherwise, +you should +be able to start from "find-system" +</p> +<pre>cl-prompt: (mk:add-registry-location "/path/to/clarity/") +cl-prompt: (mk:find-system :clarity) +System CLARITY not loaded. Shall I try loading it? y + +; Loading text file Z:\clarity\clarity.system +#<DEFSYSTEM: CLARITY> +</pre> +<p> +Now just compile and load the system.</p> +<pre>cl-prompt: (mk:compile-system :clarity) + +cl-prompt: (mk:load-system :clarity)</pre> + + <a name="gettingstarted"></a><br><br><h3>Getting Started</h3> + + <p> + In the Lispworks Listener, start by creating a handle.<br> + </p><pre>cl-prompt: (clarity:make-clarity-handle)</pre> + Now connect to your database.<br> + <pre>cl-prompt: (clarity:connect clarity::*current-clarity-handle* "DataSourceName/username/password")</pre> + + <p>From here you can call any function in the library, or you can load the GUI with the following command.</p> + <pre>cl-prompt: (clarity::start-clarity-gui)</pre> + + <p>To save your database information for future sessions, Open the clarity-database-setup-interface file and + change the three variables clarity-db-name, clarity-db-user, and clarity-db-password to reflect your setup.</p> + + + + <a name="standlone"></a><br><br><h2>Standalone Version</h2> + For the standalone graphical interface, you will need the CLARITY database and the CLARITY executable. This option is only available + for those running windows (the database, however can be on either a unix or windows machine). + Follow the steps above for downloading and installing the CLARITY DB, then just start the executable and enter the information for + the database you created. + + <a name="future"></a><br><br><h2>Future Releases</h2> + <p>In the future the CLARITY may be ported to clsql</p> + <br><br> + + + + + <hr> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <a href="mailto:samantha_PROVA_A_SPAMMARME@bioinformatics.nyu.edu">me</a>. + </p> + + </div> + </div> + +  + + <div class="content"> + <div class="text"> + + <h1>News</h1> + + <p>News in chronological order, most recent on top. + </p> + + <ul> + <li><strong>2006-8-4</strong><br> + Page updated. + <li><strong>2006-07-31</strong><br> + Page created. + </li> + </ul> + + </div> + </div> + + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + + </div></body> +</html> Added: doc/html/links.html ============================================================================== --- (empty file) +++ doc/html/links.html Wed Aug 16 16:18:39 2006 @@ -0,0 +1,98 @@ +<html> + <head> + <title>CLARITY Links</title> + <link rel="stylesheet" href="style.css"> + +  + + + </head> + +<body> +<div id="main"> + <div class="header" + style="font-family:=Verdana,Arial,Helvetica; font-size: 18px; color: #003300;"> + <strong><i>CLARITY Links</i></strong> + <div class="navigation"> + <a href="index.html" class="navigation-link-selected">Home</a> + | <a href="dictionary.html" class="navigation-link">Dictionary</a> + | <a href="downloads.html" class="navigation-link">Downloads</a> + | <a href="installation.html" class="navigation-link">Installation</a> + | <a href="links.html" class="navigation-link">Links</a> + </div> + + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + <div class="middle-bar"><img src="images/shim.gif" height="5" width="1"></div> + <div class="black-line"><img src="images/shim.gif" height="1" width="1"></div> + </div> + + <div class="content"> + <div class="text"> + + <h1>CLARITY Links</h1> + + <p>The relevant links for the <strong>CLARITY</strong> project are: + <ul> + <li>The <a href="http://www.geneontology.org"><strong>GeneOntology</strong></a> site.</li> + <li>The <a href="http://www.godatabase.org"><strong>GoDatabase</strong></a> site.</li><br> + <li>The <a href="http://sourceforge.net/project/showfiles.php?group_id=1802&package_id=7139">MK:DEFSYSTEM</a> library.</li> + <li>The <a href="http://www.lispworks.com/">LispWorks</a> site.</li> + <li><a href="http://www.common-lisp.net/">Common-Lisp.net</a>, host of the CLARITY site</li> + + </ul> + + + + <hr> + <p>Questions? Queries? Suggestions? Comments? Please direct them + at <a href="mailto:Samantha_PROVA_A_SPAMMARME@bioinformatics.nyu.edu">me</a>. + </p> + </div> + </div> +  + <div class="content"> + <div class="text"> + </div> + </div> + + <div class="copyright"> + © 2006, Samantha Kleinberg, all rights reserved. + </div> + + </div></body> +</html> Added: doc/html/style.css ============================================================================== --- (empty file) +++ doc/html/style.css Wed Aug 16 16:18:39 2006 @@ -0,0 +1,349 @@ +/* + * NYU Bioinformatics - Microarray group development + * + * Inspired by www.rhythmbox.org, (c) rhythmbox 2002 + * and http://glish.com/css/ + * + * New code, modifications + * (c) Idan Gazit 2002, and + * (c) Marco Antoniotti, 2003-2004 + * (c) Samantha Kleinberg, 2005-2006 + * NYU Bioinformatics + * Permission is hereby granted to use this style, etc etc etc. + */ + + + + +body +{ + margin:0px 5% 10px 5%; + background: #FFFFFF; + font-family: Verdana, Arial, Helvetica, sans-serif; + font-weight: normal; + color:black; +} + + +#main { + border:2px solid #000000; + background:#FFFFFF; +} + + +#main #menu { + #border-left:0px; + #border-right:1px solid #000; + #border-bottom:1px solid #000; + #border-top:1px solid #000; + float:left; + width:140px; + #background:#EEEEE0; + margin:50px 0px 0px 0px; + padding: 0px 0px 0px 10px; + position: fixed; +} + +#menu p{ +font-size:12px +font-family: Verdana, Arial, Helvetica, sans-serif; +} + + +a.navigation-link-selected +{ + text-decoration: none; + color: #ffffff; + font-weight: normal; + font-style: italic; +} + +a.navigation-link-selected:hover +{ + text-decoration: underline; + color: #ffffff; + font-weight: normal; + font-style: italic; +} + +a.navigation-link +{ + text-decoration: none; + color: #808069; + font-weight: normal; +} + +a.navigation-link:hover +{ + text-decoration: underline; + color: #ffffff; + font-weight: normal; + +} + + +a.menu-link-selected +{ + text-decoration: none; + color: #ffffff; + font-weight: normal; + font-style: italic; +} + +a.menu-link-selected:hover +{ + text-decoration: underline; + color: #ffffff; + font-weight: normal; + font-style: italic; +} + +a.menu-link +{ + text-decoration: none; + color: rgb(100, 100, 100); + font-weight: normal; +} + +a.menu:hover +{ + text-decoration: underline; + color: #ffffff; + font-weight: normal; +} + + +a.return +{ + text-decoration: none; + color: #41286f; + font-size: 8pt; + font-weight: normal; +} + +a +{ + text-decoration: underline; + color: #666600; +} + +a:hover +{ + text-decoration: underline; + color: #68548D; +} + +p +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + font-weight: normal; +} + +.header +{ + background: #CCCC99; + color: #003300; + height: 40px; + top: 0px; + width: 90%; + right: 5%; + #border: 1px solid #330066; + position: fixed; + font-family: Verdana,Arial,Helvetica; + font-size: 18px; +} + +.navigation +{ + width: 90%; + word-spacing: 5px; + position: relative; + text-align: right; + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #ffffff; + font-weight: normal; + word-spacing: 0px; + } + + + +.sidebar +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + font-weight: normal; + padding-left: 15px; + padding-right: 5px; + position: fixed; + top: 10ex; + right: 1em; + +} + +.text +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + font-weight: normal; +} + + + +li +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + font-weight: normal; +} + + +pre +{ + background: 5px; + background-color: #e0e0e0; +} + + +.label +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + text-align: center; + font-style: italic; +} + +.command +{ + font-family: Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: #000000; + background: #eae8e3; + font-weight: normal; + margin-bottom: 10px; +} + +.content +{ + background: #ffffff; + margin-top: 40px; + padding: 10px 3% 10px 155px; +} + + + +.toc +{ + font-size: 10px; + background: #ffffff; + padding: 5px; + padding-right: 5px; +} + +.middle-bar +{ + height: 5px; + background: #CC3399; +} + +.black-line +{ + height: 1px; + background: #000000; +} + +.bottom +{ + position: absolute; + right: 5px; + bottom: 5px; +} + +.copyright +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size: 10px; + color: #808080; + font-weight: normal; + padding:5px; + text-align:right; + border-color:#808080; + border-width:0px; + border-style:dotted; + border-top-width:1px; + +} + +.centerblock +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size: 12px; + color: black; + font-weight: normal; +} + + +h1 +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:18px; + color: #003300; + font-weight:bold; +} + +h2 +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:16px; + color: #003300; + font-weight:bold; +} + +h3 +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:14px; + color: #003300; + font-weight:bold; +} + +h4 +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:12px; + color: #003300; + font-weight:bold; +} + +h5 +{ + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:10px; + color: #003300; + font-weight:bold; +} + +.captionimg +{ + text-align:right; + font-style: italic; + font-weight: normal; + font-size:10px; + color: #303030; +} + +.indent +{ + padding-left: 50px; +} + +.command +{ + font-family:Courier, serif; +} Added: gui/clarity-database-setup-interface.lisp ============================================================================== --- (empty file) +++ gui/clarity-database-setup-interface.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,212 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +;;Change these three variables to the appropriate values for your setup. + +(defvar *clarity-db-name* "clarity") +(defvar *clarity-db-user* "CLDB") +(defvar *clarity-db-password* "clear") + +(capi:define-interface clarity-database-setup-interface () + () + (:panes + (notice-pane + capi:display-pane + :text '(;"" + " Please make sure that you can connect to a CLARITY database." + "") + :background :white + :visible-max-width nil) + + (clarity-db-title-pane + capi:title-pane + :text "CLARITY Database Connection" + :font (gp:make-font-description :family "Helvetica" + :size 10 + ;; :weight :bold + ;; :slant :italic + ) + :background :gray30 + :foreground :white + :visible-max-width nil + ) + + (clarity-db-name-pane + capi:text-input-pane + :reader clarity-db-name-pane + :text *clarity-db-name* + :visible-max-width 150) + + (clarity-db-user-pane + capi:text-input-pane + :reader clarity-db-user-pane + :text *clarity-db-user* ; (system:get-user-name) + :visible-max-width 150) + + (clarity-db-password-pane + capi:password-pane + :reader clarity-db-password-pane + :text *clarity-db-password* + :visible-max-width 150) + + + #+win32 + (start-system-data-source-setup-title + capi:title-pane + :text "System Data Source Configuration" + :font (gp:make-font-description :family "Helvetica" + :size 12 + ;; :weight :bold + ;; :slant :italic + ) + :background :gray30 + :foreground :white + :visible-max-width nil + ) + + #+macosx + (start-system-data-source-setup-title + capi:title-pane + :text "System Data Source Configuration" + :font (gp:make-font-description :family #+macosx "helvetica" #-macosx "Helvetica" + :size 10 + ;; :weight :bold + ;; :slant :italic + ) + :background :gray30 + :foreground :white + :visible-max-width nil + ) + + #+win32 + (start-system-data-source-setup-button + capi:push-button + :text "Start Windows ODBC Driver Manager" + :visible-max-width nil + :callback-type :none + :callback 'start-windows-data-source-setup + ) + + #+macosx + (start-system-data-source-setup-button + capi:push-button + :text "Start ODBC Driver Manager" + :visible-max-width nil + :callback-type :none + :callback 'start-macosx-data-source-setup + ) + ) + + + (:layouts + (main-layout + capi:column-layout + '(notice-pane + + clarity-db-title-pane + clarity-db-layout + + #| #+win32 |# start-system-data-source-setup-title + #| #+win32 |# start-system-data-source-setup-button + ) + ) + + (clarity-db-layout + capi:grid-layout + '("Database name" + clarity-db-name-pane + "User" + clarity-db-user-pane + "Password" + clarity-db-password-pane) + :columns 2 + :x-adjust :right + ) + + ) + + + (:default-initargs + :default-x 300 + :default-y 300 + :layout 'main-layout + :title "CLARITY Database Connections" +)) + + + +(defun start-setup-interface () + (flet ((check-fields (setup-pane) + (let ((clarity-db-name + (capi:text-input-pane-text + (clarity-db-name-pane setup-pane))) + (clarity-db-user + (capi:text-input-pane-text + (clarity-db-user-pane setup-pane))) + ) + (and clarity-db-name (string/= clarity-db-name "") + clarity-db-user (string/= clarity-db-user "")) + )) + ) + (multiple-value-bind (setup-pane valid-p) + (capi:popup-confirmer (make-instance 'clarity-database-setup-interface) + "CLARITY Database Connection Setup" + ;; :ok-check #'check-fields + :title "CLARITY" + ) + (when valid-p + (let ((clarity-db-name + (capi:text-input-pane-text + (clarity-db-name-pane setup-pane))) + (clarity-db-user + (capi:text-input-pane-text + (clarity-db-user-pane setup-pane))) + (clarity-db-password + (capi:text-input-pane-text + (clarity-db-password-pane setup-pane))) + ) + (concatenate 'string clarity-db-name "/" clarity-db-user "/" clarity-db-password) + )) + )) + ;(capi:display (make-instance 'clarity-database-setup-interface) + ) +#+win32 +(defun start-windows-data-source-setup () + (handler-case + (system:call-system "C:\\WINDOWS\\system32\\odbcad32.exe") + (error (e) + (declare (ignore e)) + (capi:display-message "Sorry, cannot start the ODBC driver manager."))) + ) + + +#+macosx +(defun start-macosx-data-source-setup () + (handler-case + (system:call-system "/Applications/Utilities/ODBC\\ Administrator.app/Contents/MacOS/ODBC\\ Administrator") + (error (e) + (declare (ignore e)) + (capi:display-message "Sorry, cannot start the ODBC driver manager."))) + ) + + ;;; end of file -- clarity-database-setup-interface.lisp -- Added: gui/clarity-gui.system ============================================================================== --- (empty file) +++ gui/clarity-gui.system Wed Aug 16 16:18:39 2006 @@ -0,0 +1,52 @@ +;;; -*- Mode: Lisp -*- + + +;;; Setting up the logical pathname. + +(eval-when (:load-toplevel :execute) + (setf (logical-pathname-translations "CLARITY") + `(("*.*" ,(make-pathname :name :wild :type :wild + :defaults *load-pathname*)) + ("*.*.*" ,(make-pathname :name :wild :type :wild :version :wild + :defaults *load-pathname*)) + ("**;*.*" ,(merge-pathnames + (make-pathname :directory '(:relative :wild-inferiors) + :name :wild + :type :wild + :version :wild) + *load-pathname* + )) + ("**;*.*.*" ,(merge-pathnames + (make-pathname :directory '(:relative :wild-inferiors) + :name :wild + :type :wild + :version :wild + :version :wild) + *load-pathname* + )) + ))) + + + +;;; Adding registry locations. + +#|(eval-when (:load-toplevel :execute) + (mk:add-registry-location + (merge-pathnames (pathname "gui/") + (make-pathname :name nil :type nil + :defaults *load-pathname*))) + + (mk:add-registry-location (translate-logical-pathname "CLARITY:")))|# + + +(mk:defsystem "CLARITY-GUI" + :components ("clarity-gui-package" + "insert-data-interface" + "clarity-interface" + "clarity-interface-functions" + "start-gui" + "clarity-database-setup-interface" + ) + ) + +;;; end of file -- clarity-gui.system -- Added: gui/clarity-interface-functions.lisp ============================================================================== --- (empty file) +++ gui/clarity-interface-functions.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,261 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + + +(eval-when (:compile-toplevel :load-toplevel :execute) + (require "sql") + (require "odbc")) + + +#.(sql:enable-sql-reader-syntax) + + +(defconstant *up* 0) +(defconstant *down* 1) +(defconstant *neutral* 2) +(defconstant *inactive* 3) + +(defclass phylogeny-item() + ((tree-id :accessor phylogeny-tree-id :initarg :phylogeny-tree-id) + (data-id :accessor phylogeny-data-id :initarg :phylogeny-data-id)) + ) + +(defclass phylogeny-term() + ((term-name :accessor term-name :initarg :term-name) + (data-id :accessor data-id :initarg :data-id) + )) + +(defclass phylogeny-window() + ((term :accessor phylogeny-window-term :initarg :phylogeny-window-term) + (window-start :accessor phylogeny-window-start :initarg :phylogeny-window-start) + (window-end :accessor phylogeny-window-end :initarg :phylogeny-window-end) + (regulation :accessor phylogeny-window-reg :initarg :phylogeny-window-reg) + )) + +(defclass phylogeny-associations() + () + ) + + +(defmethod insert-file-popup ((interface clarity-interface)) + (let ((idi (make-instance 'insert-data-interface))) + (when (capi:display-dialog idi) + (cond ((eq t (capi:button-enabled + (probe-check-box idi))) + (insert-with-probes (clarity-handle interface) + (file-location idi) + (capi:text-input-pane-text (file-date-input idi)))) + (t (insert (clarity-handle interface) + (file-location idi) + (capi:text-input-pane-text (file-date-input idi))))) + ) + )) + + +(defmethod get-filename ((interface insert-data-interface)) + (let ((file (capi:prompt-for-file "Select data file to insert."))) + (setf (file-location interface) file) + + (capi:apply-in-pane-process + (file-location-pane interface) + #'(setf capi:display-pane-text) + (print-partial-filename file) (file-location-pane interface)) + ) + ) + +(defmethod get-phylogeny-root ((clh clarity-handle)) + (let ((root (get-root clh))) + (make-instance 'phylogeny-item + :phylogeny-tree-id root + :phylogeny-data-id (first (sql:with-transaction + (sql:select [|timecourse_data_id|] + :from [|tree|] + :where [= [id] root] + :database (connection clh) + :flatp t + ))) + ))) + +(defmethod get-phylogeny-children ((node phylogeny-item)) + (let ((children (get-children (phylogeny-tree-id node)))) + (if children + (loop for c in children + collecting (make-instance 'phylogeny-item + :phylogeny-tree-id c + :phylogeny-data-id (first (sql:with-transaction + (sql:select [|timecourse_data_id|] + :from [|tree|] + :where [= [id] c] + :database (connection *current-clarity-handle*) + :flatp t + ))))) + nil + ))) + +(defmethod make-phylogeny-terms-roots ((clh clarity-handle) node-id term-list) + (let ((timecourse-id (first (sql:with-transaction + (sql:select [|timecourse_data_id|] + :from [|tree|] + :where [= [id] node-id] + :database (connection clh) + :flatp t)))) + ) + ;;is consensus + (loop for term in term-list + collecting (make-instance 'phylogeny-term + :term-name term + :data-id timecourse-id))) + ) + + +(defmethod get-phylogeny-terms-children (tree-node) + (cond ((typep tree-node 'phylogeny-term) + (loop for (start end num) in (sql:select [|window_start|] [|window_end|] [|data|] + :from [|numerical_data|] + :where [and [= [|timecourse_data_id|] (data-id tree-node)] + [= [|term_name|] (term-name tree-node)]] + :database (connection *current-clarity-handle*) + :distinct t + ) + collecting (make-instance 'phylogeny-window + :phylogeny-window-term tree-node + :phylogeny-window-start start + :phylogeny-window-end end + :phylogeny-window-reg (cond ((> num 0) *up*) + ((< num 0) *down*) + ((= num 0) *neutral*) + (t *inactive*)) + ))) + ((typep tree-node 'phylogeny-window) + (split-sequence:split-sequence #\Space (first (sql:with-transaction + (sql:select [|probe_ids|] + :from [|numerical_data|] + :where [and [= [term_name] (term-name (phylogeny-window-term tree-node))] + [= [window_start] (phylogeny-window-start tree-node)] + [= [window_end] (phylogeny-window-end tree-node)] + [= [timecourse_data_id] + (data-id (phylogeny-window-term tree-node))]] + :database (connection *current-clarity-handle*) + :flatp t))) + :remove-empty-subseqs t)) + (t nil) + )) + +(defmethod phylogeny-window-icon (node) + (cond ((typep node 'phylogeny-window) + (phylogeny-window-reg node)) + (t 4)) + ) + +(defmethod phylogeny-terms-print-function (node) + (cond ((typep node 'phylogeny-term) + (term-name node)) + ((typep node 'phylogeny-window) + (format nil "Window ~a-~a" (phylogeny-window-start node) (phylogeny-window-end node)) + ) + (t node) + ) + ) + +(defmethod database-switch-callback (data (interface clarity-interface)) + (cond ((equal data "View all entries") + (setf (capi:collection-items + (database-all-entries interface)) (get-all-data (clarity-handle interface))) + (capi:apply-in-pane-process + (database-switchable interface) + #'(setf capi:switchable-layout-visible-child) + (database-all-entries interface) (database-switchable interface)) + ) + + ((equal data "Search entries") + (capi:apply-in-pane-process + (database-switchable interface) + #'(setf capi:switchable-layout-visible-child) + (database-single-entry interface) (database-switchable interface))) + )) + +;;should store nodes locally as in cl-godb, will fix this later +(defmethod phylogeny-select-callback ((item phylogeny-item) interface) + (let* ((node-id (phylogeny-tree-id item)) + (children (get-children node-id))) + (if children + ;;is internal node + (let ((consensus (get-node-terms (clarity-handle interface) node-id))) + (setf (capi:collection-items + (consensus-detail interface)) + consensus) + + (setf (capi:tree-view-roots (left-child-detail interface)) + (make-phylogeny-terms-roots (clarity-handle interface) + (first children) + (set-difference (get-node-terms (clarity-handle interface) + (first children)) + consensus + :test #'equal))) + (setf (capi:tree-view-roots (right-child-detail interface)) + (make-phylogeny-terms-roots (clarity-handle interface) + (second children) + (set-difference (get-node-terms (clarity-handle interface) + (second children)) + consensus + :test #'equal)))) + ;;is leaf + (leaf-callback node-id interface) + + ))) + +(defmethod leaf-callback (node-id interface) + (setf (capi:collection-items + (leaf-terms interface)) + (flatten (get-node-terms (clarity-handle interface) node-id))) + (clear-node-data-panes interface) + ) + +(defmethod clear-node-data-panes (interface) + (setf (capi:collection-items + (consensus-detail interface)) + nil) + (setf (capi:tree-view-roots + (right-child-detail interface)) + nil) + (setf (capi:tree-view-roots + (left-child-detail interface)) + nil) + ) + + +(defun print-partial-filename (f) + (let* ((f (pathname f)) + (pd (pathname-directory f)) + (pn (pathname-name f)) + (pt (pathname-type f)) + (last-pd (first (last pd))) + ) + (format nil + "~@[.../~A/~]~@[~A.~A~]" + last-pd + pn + pt))) + + + Added: gui/clarity-interface.lisp ============================================================================== --- (empty file) +++ gui/clarity-interface.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,190 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +(defvar *my-image-list* + (make-instance 'capi:image-list + :image-sets (list (capi:make-general-image-set + :id #.(gp:read-external-image (lispworks:current-pathname "icons/icons.bmp")) + :image-count 4)) + :image-width 16 + :image-height 16)) + + +(capi:define-interface clarity-interface () + ((clarity-handle :accessor clarity-handle + :initarg :clarity-handle)) + (:panes + (graph-pane-1 + capi:graph-pane + :print-function (lambda (x) (princ-to-string (phylogeny-data-id x))) + :roots (list (get-phylogeny-root *current-clarity-handle*)) + :children-function (lambda (x) (get-phylogeny-children x)) + :layout-function :top-down + :selection-callback 'phylogeny-select-callback + :callback-type :item-interface + :accessor phylogeny-pane) + + (database-buttons + capi:push-button-panel + :title "Database Options" + ; :items '("View all entries" "Search entries") + :items '("View all entries") + :layout-class 'capi:column-layout + :callback-type :data-interface + :selection-callback 'database-switch-callback + ) + + + (database-all-entries + capi:multi-column-list-panel + ; :items + :visible-min-width 300 + :visible-min-height :text-height + :columns '((:title "ID" + :adjust :left + :width (character 15)) + (:title "Filename" + :adjust :left + :visible-min-width (character 20)) + (:title "Date" + :adjust :left + :width (character 20))) + ;:selection-callback + ;mclp-header-callback + :accessor database-all-entries + ) + + (database-single-entry + capi:grid-layout + :accessor database-single-entry + ) + + (database-switchable + capi:switchable-layout + :description '(database-all-entries database-single-entry) + :accessor database-switchable + ) + + (leaf-terms + capi:list-panel + :accessor leaf-terms + :title "Terms" + ) + + (left-child-detail + capi:tree-view + :title "Left child" + :accessor left-child-detail + :children-function (lambda (x) (get-phylogeny-terms-children x)) + ;:children-function (lambda (x) nil) + :print-function (lambda (x) (phylogeny-terms-print-function x)) + :image-lists (list :normal *my-image-list*) + :image-function #'(lambda (x) (phylogeny-window-icon x)) + ) + + (right-child-detail + capi:tree-view + :title "Right child" + :accessor right-child-detail + :children-function (lambda (x) (get-phylogeny-terms-children x)) + ;:children-function (lambda (x) nil) + :print-function (lambda (x) (phylogeny-terms-print-function x)) + :image-lists (list :normal *my-image-list*) + :image-function #'(lambda (x) (phylogeny-window-icon x)) + ) + + + (consensus-detail + capi:list-panel + :title "Consensus" + :accessor consensus-detail + ) + + ) + (:layouts + (column-layout-1 + capi:column-layout + '(tab-layout-1)) + (tab-layout-1 + capi:tab-layout + () + :items '(("Database" database-layout) ("Phylogeny" phylogeny-layout)) + :print-function 'car + :visible-child-function 'second) + (database-layout + capi:row-layout + '(database-buttons + database-switchable) + ) + + (internal-node-detail + capi:row-layout + '(left-child-detail consensus-detail right-child-detail) + ) + + (leaf-layout + capi:row-layout + '(leaf-terms) + ) + + (phylogeny-detail + capi:tab-layout + () + :items '(("Leaf node" leaf-layout) + ("Internal node" internal-node-detail)) + :print-function 'car + :visible-child-function 'second + ) + + (phylogeny-layout + capi:column-layout + '(graph-pane-1 + phylogeny-detail)) + + (column-layout-3 + capi:column-layout + '(graph-pane-1 + phylogeny-detail))) + + (:menu-bar file edit) + (:menus + (edit + "Edit" + ()) + (file + "File" + ((:component + ( ("Insert" :callback 'insert-file-popup + :callback-type :interface)))))) + + (:default-initargs + :best-height 280 + :best-width 300 + :layout 'column-layout-1 + :title "CLARITY")) + +(defun start-clarity-interface () + (let ((gui (make-instance 'clarity-interface + :clarity-handle *current-clarity-handle*))) + (capi:display gui) + )) Added: gui/icons/base.bmp ============================================================================== Binary file. No diff available. Added: gui/icons/down.bmp ============================================================================== Binary file. No diff available. Added: gui/icons/icons.bmp ============================================================================== Binary file. No diff available. Added: gui/icons/inactive.bmp ============================================================================== Binary file. No diff available. Added: gui/icons/neutral.bmp ============================================================================== Binary file. No diff available. Added: gui/icons/up.bmp ============================================================================== Binary file. No diff available. Added: gui/insert-data-interface.lisp ============================================================================== --- (empty file) +++ gui/insert-data-interface.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,89 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +(capi:define-interface insert-data-interface () + ((file-location :accessor file-location + :initarg :file-location)) + (:panes + (insert-form + capi:title-pane + :text "Fill out form") + (file-location-1 + capi:title-pane + :text "File location:") + (file-location-input-1 + capi:display-pane + :accessor file-location-pane + ) + (file-location-button-1 + capi:push-button + :text "Find file" + :selection-callback 'get-filename + :callback-type :interface + ) + (file-date-1 + capi:title-pane + :text "Creation date") + (file-date-input-1 + capi:text-input-pane + :accessor file-date-input) + (spacer + capi:title-pane + :text "") + (spacer-2 + capi:title-pane + :text "") + (spacer-3 + capi:title-pane + :text "") + + (probe-check-box + capi:check-button + :text "Check if data file includes gene information." + :accessor probe-check-box + ) + + (ok-cancel-panel + capi:push-button-panel + :items '("OK" "Cancel") + :callback-type :data + :callbacks '(capi:exit-dialog + capi:abort-dialog) + :max-height t + :max-width t)) + (:layouts + (column-layout-1 + capi:column-layout + '(insert-form grid-layout-1)) + (grid-layout-1 + capi:grid-layout + '(file-location-1 file-location-input-1 file-location-button-1 + file-date-1 file-date-input-1 spacer + probe-check-box spacer-3 spacer-3 + spacer-2 ok-cancel-panel) + :columns 3)) + (:default-initargs + :best-height 89 + :best-width 424 + :layout 'column-layout-1 + :title "Insert-data-interface")) Added: gui/start-gui.lisp ============================================================================== --- (empty file) +++ gui/start-gui.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,122 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +(in-package "CLARITY") + +(eval-when (:compile-toplevel :load-toplevel :execute) + (require "sql") + (require "odbc")) + + +#.(sql:enable-sql-reader-syntax) + + +;;; Environment setting functions. + +(defun setup-clarity-logical-pathnames () + (let* ((command (first system:*line-arguments-list*)) + (executable-location + (make-pathname :name nil + :type nil + :defaults (pathname command))) + ) + (setf (logical-pathname-translations "CLARITY") + `(("*.*" ,(make-pathname :name :wild + :type :wild + :defaults executable-location)) + ("*.*.*" ,(make-pathname :name :wild + :type :wild + :version :wild + :defaults executable-location)) + ("**;*.*" ,(merge-pathnames + (make-pathname :name :wild + :type :wild + :directory (list :relative :wild-inferiors)) + executable-location)) + ("**;*.*.*" ,(merge-pathnames + (make-pathname :name :wild + :type :wild + :version :wild + :directory (list :relative :wild-inferiors)) + executable-location)) + ) + ))) + + + +;;; Startup functions. + + +(defvar *clarity-init-file* + (make-pathname :name ".clarity-init" + :type nil + :defaults (user-homedir-pathname))) + +(defvar *clarity-init-file-dos* + (make-pathname :name "_clarity-init" + :type nil + :defaults (user-homedir-pathname))) + + +(defun start-clarity-gui (&key(init-file (list *clarity-init-file* + *clarity-init-file-dos*)) + data-file + (reset-logical-pathnames-p t) + ) + (flet ((load-init-file (init-file) + (let ((*package* (find-package "CLARITY"))) + (load init-file :print nil :verbose nil :if-does-not-exist nil))) + ) + (etypecase init-file + (list (some #'load-init-file init-file)) + ((or string pathname) (load-init-file init-file))) + + + (capi:display-message "Starting CLARITY.") + + (clarity:make-clarity-handle) + (clarity:connect clarity::*current-clarity-handle* (clarity::start-setup-interface)) + (capi:display-message "DBS connected.") + + (let ((gui (make-instance 'clarity-interface + :clarity-handle clarity::*current-clarity-handle*))) + (capi:display gui) + (when reset-logical-pathnames-p + (setup-clarity-logical-pathnames)) + (capi:execute-with-interface + gui + (lambda () + (etypecase init-file + (list (some #'load-init-file init-file)) + ((or string pathname) (load-init-file init-file))) + (when reset-logical-pathnames-p + (setup-clarity-logical-pathnames)) + + )) + + (when data-file + (load data-file :print nil :verbose nil)) + gui))) + + +#.(sql:disable-sql-reader-syntax) + +;;; end of file -- start-gui.lisp -- Added: sql/clarity.sql ============================================================================== --- (empty file) +++ sql/clarity.sql Wed Aug 16 16:18:39 2006 @@ -0,0 +1,67 @@ +--************************************************** +--** SQl script for creating CLARITY tables ** +--** clarity.sql ** +--************************************************** + + +--** table for storing phylogenetic tree ** + + +CREATE DATABASE clarity; + +USE clarity; + +CREATE TABLE timecourse_data ( + id INTEGER NOT NULL AUTO_INCREMENT, + datafile_path VARCHAR(100) NOT NULL, + creation_date VARCHAR(45) NOT NULL, + association_file VARCHAR(100) NOT NULL, + patient_id INTEGER, + PRIMARY KEY (id) +); + + +--** table for storing gantt charts ** +CREATE TABLE gantt_chart ( + id INTEGER NOT NULL AUTO_INCREMENT, + timecourse_data_id INTEGER DEFAUlT '0', + term_name VARCHAR(200), + sequence VARCHAR(45) NOT NULL, + PRIMARY KEY(id) +); + + +--** table for storing numerical data ** +CREATE TABLE numerical_data ( + id INTEGER NOT NULL AUTO_INCREMENT, + timecourse_data_id INTEGER, + term_name VARCHAR(100), + window_start FLOAT, + window_end FLOAT, + data FLOAT, + probe_ids TEXT, + PRIMARY KEY(id) +); + + +--** table for storing phylogenetic tree ** +CREATE TABLE tree ( + id INTEGER NOT NULL AUTO_INCREMENT, + timecourse_data_id INTEGER DEFAULT '0', + node_left INTEGER DEFAULT '0', + node_right INTEGER DEFAULT '0', + is_root INTEGER DEFAULT '0', + consensus_id INTEGER DEFAULT '0', + PRIMARY KEY(id) +); + +--** table for storing consensus sequences ** +--** for phylogenetic tree ** + +CREATE TABLE consensus ( + id INTEGER NOT NULL AUTO_INCREMENT, + tree_id INTEGER DEFAULT '0', + term_name VARCHAR(100) NOT NULL, + sequence VARCHAR(45) NOT NULL, + PRIMARY KEY(id) +); Added: utilities/delivery/clarity-4.ico ============================================================================== Binary file. No diff available. Added: utilities/delivery/clarity-icon-3.bmp ============================================================================== Binary file. No diff available. Added: utilities/delivery/clarity-icon-3.ico ============================================================================== Binary file. No diff available. Added: utilities/delivery/clarity-icon-4.bmp ============================================================================== Binary file. No diff available. Added: utilities/delivery/clarity-icon-4.ico ============================================================================== Binary file. No diff available. Added: utilities/delivery/clarity.ico ============================================================================== Binary file. No diff available. Added: utilities/delivery/delivery-script.fsl ============================================================================== Binary file. No diff available. Added: utilities/delivery/delivery-script.lisp ============================================================================== --- (empty file) +++ utilities/delivery/delivery-script.lisp Wed Aug 16 16:18:39 2006 @@ -0,0 +1,143 @@ +;;; -*- Mode: Lisp -*- + +#|CLARITY: Common Lisp Data Alignment Repository +Copyright (c) 2006 Samantha Kleinberg +All rights reserved. + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU +Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser +General Public License for more details. + +You should have received a copy of the GNU Lesser General Public License along with this library; +if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +contact: Samantha AT Bioinformatics DOT nyu DOT edu +715 Broadway, 10th floor +New York, NY 10003|# + +;;; delivery-script.lisp -- Lispworks dependent delivery script. + +(in-package "COMMON-LISP-USER") + + +;;;=========================================================================== +;;; Setting up the environment. + +(defvar *_mxa-init-file* (merge-pathnames (make-pathname :name ".lispworks") + (user-homedir-pathname))) + + +(unless (find-package "MAKE") + (load *_mxa-init-file*) + ) + + +(defvar *clarity-system-file* + (pathname "z:/lisp/clarity/clarity.system")) + + +(loop until (and (or (stringp *clarity-system-file*) + (pathnamep *clarity-system-file*)) + (probe-file *clarity-system-file*)) + do (cerror ";;; Enter the full path of the CLARITY.system file: " + ";;; CLARITY system file ~S could not be found." + (namestring *clarity-system-file*)) + do (setf *clarity-system-file* (read))) + + +(defvar *clarity-gui-system-file* + (pathname "z:/lisp/clarity/gui/impl-dependent/lwcapi/clarity-gui.system")) + + +(loop until (and (or (stringp *clarity-gui-system-file*) + (pathnamep *clarity-gui-system-file*)) + (probe-file *clarity-gui-system-file*)) + do (cerror ";;; Enter the full path of the CLARITY-GUI.system file: " + ";;; CLARITY-GUI system file ~S could not be found." + (namestring *clarity-gui-system-file*)) + do (setf *clarity-gui-system-file* (read))) + +(defparameter *clarity-application-file* "clarity") + +(proclaim '(optimize (debug 1) (speed 3) (space 2))) ; Turn on Tail Merge. + + +;;;--------------------------------------------------------------------------- +;;; Platform dependent initializations. + +#+(and macosx cocoa) +(compile-file-if-needed (sys:example-file "configuration/macos-application-bundle") + :load t) + +#+(and macosx cocoa) +(setf *xssys-application-file* + (write-macos-application-bundle "~/Applications/XSSYS.app")) + + +;;;=========================================================================== +;;; Loading all the necessary bits and pieces of the application. + +;;; Ensure all the features are loaded. + +(require "sql") +(require "odbc") + +(pushnew :clarity-gui *features*) +(pushnew :clarity *features*) + + + +;;; Load the .system file and compile it. + +(load *clarity-system-file*) +(mk:load-system "Clarity") + +(load *clarity-gui-system-file*) +(mk:load-system "CLARITY-GUI") + + +;;; Ensure that the stupid pprinter is loaded. + +(format t (formatter "~3%;;;~75,,,'=A~@ + ;;; Starting delivery.~@ + ;;; CLARITY system loaded.~%") + #\=) + + +;;; Ensure that all the DBS are disconnected. + +;(clarity::disconnect-clarity-dbs) + + +;;; Turn off interactive debugger switches. + +;(setf clarity::*clarity-has-debugger-present* nil) + + +;;; Deliver the 'clarity' application. + +(deliver 'clarity::start-clarity-gui + + *clarity-application-file* 0 + :interface :capi + :keep-pretty-printer t + :versioninfo (list :binary-version #x0000000100000000 + :version-string "CLARITY version 1.0.0.0" + :company-name "NYU Courant Bioinformatics Group" + :product-name "CLARITY" + :file-description + (format nil + "CLARITY.") + :legal-copyright + (format nil "Copyright (c) 2006 Samantha Kleinberg~@ + All rights reserved.") + ) + :icon-file "clarity-icon-3.ico" + ) +(quit) + +;;; end of file -- delivery-script.lisp -- Added: utilities/delivery/lwdeli.bat ============================================================================== --- (empty file) +++ utilities/delivery/lwdeli.bat Wed Aug 16 16:18:39 2006 @@ -0,0 +1,8 @@ +@echo off +rem lwdeli.bat -- Delivery script for LW. + +echo ;;; GOALIE: building application... + +C:\PROGRA~1\XANALYS\LISPWO~1\LISPWO~1.exe -init delivery-script.lisp + +rem end of file -- lwdeli.bat --

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