[Clarity-cvs] r1 - doc doc/html doc/html/dictionary doc/html/images gui gui/icons sql utilities utilities/delivery

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. 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 \ No newline at end of file Added: LGPL.TXT ============================================================================== --- (empty file) +++ LGPL.TXT Wed Aug 16 16:18:39 2006 @@ -0,0 +1,106 @@ +TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + +0. This License Agreement applies to any software library or other program which contains a notice placed by the copyright holder or other authorized party saying it may be distributed under the terms of this Lesser General Public License (also called "this License"). 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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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + + </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> + +<!-- ;;; Items from database-functions--> + <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> + + <!-- ;;; Items from alignment-functions--> + <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> + +<!-- +;;; Copyright (c) 2006 Samantha Kleinberg, All rights reserved. +;;; +;;; Permission to use, modify, and redistribute this code is hereby +;;; granted. +;;; The code is provided AS IS with NO warranty whatsoever. The author +;;; will not be held liable etc etc etc etc etc. +--> + + + + <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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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.  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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + </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"> + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + + </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> + + +<!-- +;;; Copyright (c) 2006 Samantha Kleinberg, All rights reserved. +;;; +;;; Permission to use, modify, and redistribute this code is hereby +;;; granted. +;;; The code is provided AS IS with NO warranty whatsoever. The author +;;; will not be held liable etc etc etc etc etc. +--> + + + + <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"/> + + + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + + </style> +<![endif]--> + + + + </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_@_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"/> + + + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + + </style> +<![endif]--> + + + + </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_@_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"> + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + + </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") + +<!---- <p>Get the GoDB. The latest version of the GoDB can be downloaded from the + <a href="http://www.godatabase.org/dev/database/">Gene Ontology Database Downloads</a> page. + You will need the assocdb-table files. Continue below with the section appropriate for your system. ----> + + <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> + +<!-- +;;; Copyright (c) 2006 Samantha Kleinberg, All rights reserved. +;;; +;;; Permission to use, modify, and redistribute this code is hereby +;;; granted. +;;; The code is provided AS IS with NO warranty whatsoever. The author +;;; will not be held liable etc etc etc etc etc. +--> + + + <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"> + + <!--[if IE]> +<style> +.header { + border: 0px; + width: 100%; +} + +#main #menu { + margin:10px 0px 0px 0px; +} + +.content +{ + background: #ffffff; + margin-top: 0px; + padding: 0px 0px 10px 155px; +} + +.navigation +{ + width: 90%; + top: -1px; + word-spacing: 5px; + position: relative; + text-align: right; + } + +</style> +<![endif]--> + + + </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> + +<!-- +;;; Copyright (c) 2006 Samantha Kleinberg, All rights reserved. +;;; +;;; Permission to use, modify, and redistribute this code is hereby +;;; granted. +;;; The code is provided AS IS with NO warranty whatsoever. The author +;;; will not be held liable etc etc etc etc etc. +--> + + <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 --