Copyright (C) 2011  N.D. Price Lab
 
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program 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 Affero General Public License for more details.
 
You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Modules
		copy AUREA.learner.dirac AUREA.learner.ktsp os pyBabel shutil socket sys time _tkinter AUREA.learner.tsp AUREA.learner.tst urllib2

Classes
		Controller   class Controller     #thread_message_queue     Methods defined here: __init__(self, workspace) This is the controller (MVC design pattern) for the GUI. workspace is the folder that contains the config file and where temporary files and data files will be brought. addSOFTFile(self, softFile) addUnclassified(self, table, sample_name) Adds an unclassified sample to the data package buildDataPackage(self) Merges all the data tables into one package from which we pull our data for learning buildDataTables(self) Builds a table for each data file classifyAdaptive(self) classifyDirac(self) classifyTSP(self) classifyTST(self) classifykTSP(self) clearClassSamples(self) Removes samples from any classifications clearLearningAlg(self) Set all learning algorithms to None. Happens when we change something further up the dependency createClassification(self, page) Gets and sets the class labels crossValidateAdaptive(self, target_acc, maxtime) crossValidateDirac(self) crossValidateKTSP(self) crossValidateTSP(self) crossValidateTST(self) downloadSOFT(self, softfilename) Note raises urllib2.URLError when the download attempt fails getClassificationInfo(self) Returns the names and sizes of the partitioned classes  (c1name, c1size, c2name, c2size) ('',0,'',0) is returned if classifications have not been created getCrossValidationResults(self) Returns the cross validation accuracy of the learners over  the training set (TSP,kTSP,TST,DiRaC, Adaptive) getDataPackagingResults(self) Returns a list of tuples with (genes in merge, probes in merge) getLearnerAccuracy(self) Returns the apparent accuracy of the learners over the training set (TSP,kTSP,TST,DiRaC, Adaptive) getNetworkInfo(self) getSampleInfo(self, table, sample_id) Gets the information about a sample if it is available getSamples(self) Returns a list of strings describing all available samples in the data tables [ '[dt1].samp_name', '[dt2].samp_name', ...] getSubsets(self) Returns a list of 2-tuples,  [ (description, list of sample names formatted to match getSamples), ...] getUntrainedSamples(self) This is basically getSamples with the training set removed initWorkspace(self) Initialize the workspace files. Copy from the system any necessary files. (config, gene_syn, etc) DEPRECATED!!!! loadFiles(self) Loads all of the specified files parseNetworkFile(self) Parse network file and add networks to datapackage parseSOFTFiles(self) adds SOFTparser objects to softparser partitionClasses(self, class1List, class2List) Puts the samples into their chosen classes setApp(self, app) setGeneNetworkFile(self, gnFile) setSOFTFile(self, softFile) DEPRECATED setSynonymFile(self, sFile) trainAdaptive(self, target_accuracy, maxTime) trainDirac(self, crossValidate=False) trainTSP(self, crossValidate=False) Performs the training of TSP trainTST(self, crossValidate=False) Performs the training of tst trainkTSP(self, crossValidate=False) Performs the training of k-TSP unloadFiles(self) updateState(self, dependency, satisfied) Given a dependency, update to satisfied in global dependencies, propagating change

Data
		ACTIVE = 'active' ALL = 'all' ANCHOR = 'anchor' ARC = 'arc' BASELINE = 'baseline' BEVEL = 'bevel' BOTH = 'both' BOTTOM = 'bottom' BROWSE = 'browse' BUTT = 'butt' CASCADE = 'cascade' CENTER = 'center' CHAR = 'char' CHECKBUTTON = 'checkbutton' CHORD = 'chord' COMMAND = 'command' CURRENT = 'current' DISABLED = 'disabled' DOTBOX = 'dotbox' E = 'e' END = 'end' EW = 'ew' EXCEPTION = 8 EXTENDED = 'extended' FALSE = 0 FIRST = 'first' FLAT = 'flat' GROOVE = 'groove' HIDDEN = 'hidden' HORIZONTAL = 'horizontal' INSERT = 'insert' INSIDE = 'inside' LAST = 'last' LEFT = 'left' MITER = 'miter' MOVETO = 'moveto' MULTIPLE = 'multiple' N = 'n' NE = 'ne' NO = 0 NONE = 'none' NORMAL = 'normal' NS = 'ns' NSEW = 'nsew' NUMERIC = 'numeric' NW = 'nw' OFF = 0 ON = 1 OUTSIDE = 'outside' PAGES = 'pages' PIESLICE = 'pieslice' PROJECTING = 'projecting' RADIOBUTTON = 'radiobutton' RAISED = 'raised' READABLE = 2 RIDGE = 'ridge' RIGHT = 'right' ROUND = 'round' S = 's' SCROLL = 'scroll' SE = 'se' SEL = 'sel' SEL_FIRST = 'sel.first' SEL_LAST = 'sel.last' SEPARATOR = 'separator' SINGLE = 'single' SOLID = 'solid' SUNKEN = 'sunken' SW = 'sw' StringTypes = (<type 'str'>, <type 'unicode'>) TOP = 'top' TRUE = 1 TclVersion = 8.5 TkVersion = 8.5 UNDERLINE = 'underline' UNITS = 'units' VERTICAL = 'vertical' W = 'w' WORD = 'word' WRITABLE = 4 X = 'x' Y = 'y' YES = 1 wantobjects = 1