A B C D E F G H I K L M N O P R S T U V W

A

accept(File) - Method in class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
Returns true iff f is not null and a directory or has a non-null extension in validExt
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.chromviewer.ChromEnrichmentTable
Handles interface actions
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
to process a button press
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Handles actions on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Responds to interface actions
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.core.ListDialog
Handle clicks on the Set and Cancel buttons.
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREM_IO
Responds to buttons being pressed on the main input interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Responds to buttons being pressed on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_EdgeTable
Responds to buttons being pressed on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStatic
Responds to buttons being pressed on the input interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Responds to actions on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOFilter
Responds to buttons being pressed
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Responds to buttons being pressed on the table
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOSplitTable
Responds to buttons being pressed on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOTable
Responds to actions to the GO table interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions
Responds to actions on the interface window
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_KeyInputs
Responds to buttons being pressed on the interface window
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_Predict
Responds to actions on the window
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Responds to actions on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_StaticSummaryTable
Responds to actions on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.DefineGeneSet
Controls actions for various buttons being pressed on the define gene set interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.FilteredTable
Handles response to buttons being pressed
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.GenePlotPanel
Responds to actionPerformed events
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.GeneTable
Responds to button being pressed
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Responds to interface actions on the table
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.GOTable
Responds to interface actions on the table
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.GOTableExpected
Responds to interface actions on the interface
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Responds to buttons being pressed
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.MainTable
Responds to buttons being pressed
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.SortTable
Responds to interace actions on this interface window
actionPerformed(ActionEvent) - Method in class edu.cmu.cs.sb.stem.ST
Manages the responds to actions on the interface
addActiveGenes(String[]) - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Adds the set of genes in names to those currently displayed by the chromosome viewer
addBaseGenes(String[], ArrayList) - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Adds to the base set of genes all genes in input names and alnames
addExtension(String) - Method in class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
Adds szext into validExt
addExtraToFilter(GoAnnotations) - Method in class edu.cmu.cs.sb.core.DataSetCore
Add those genes from tga.extragenes that were filtered to thtFiltered
addGene(Gene, String, Paint) - Method in class edu.cmu.cs.sb.chromviewer.ChromRectangle
Adds a gene to this chromosome
addgenesgo(String, String, HashSet, HashSet, HashMap) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Add go annotations to szannotation or its cross-reference for every entry in szGoPortion delimited by tabs, semiclons, commas, pipes, or double quotes.
addgenesgocategory(String, HashSet, HashSet) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Adds szcategory or its alternative ID to gocategories, provide it is not in removedterms also if this category has not been seen before add the ID and its name if available to htGO.
addGOLabels(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOFilter
Adds p-value labels meeting the significance threshold to the interface
addOfficialLine(StringTokenizer, HashSet, HashSet, HashMap, HashMap) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Maps annotations to GO categories for offical 15 column GO annotation files.
addprobegenemap(String, String, HashMap, HashSet) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Adds a mapping of probe symbols to gene IDs, where the probe symbols are the sub-entries while the gene entry is the full field to htProbetoGene.
addSetLabels(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Adds label for enrichment of the selected set of genes for paths or splits based on the specified criteria
addSetLabels(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStatic
Adds significance labels to the main interface based on the specificed settings of the parameters
algoAll - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Arraylist of hash sets of GO categories of each unique gene
algoAllbase - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Arraylist of hash sets of GO categories of each unique gene
allButton - Variable in class edu.cmu.cs.sb.core.ListDialog
 
ALLPERMSTHRESH - Static variable in class edu.cmu.cs.sb.stem.STEM_DataSet
 
ASCENDING - Static variable in class edu.cmu.cs.sb.core.TableSorter
 
assignall0() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Sets all genes to be assigned to profile index 0
averageAndFilterDuplicates() - Method in class edu.cmu.cs.sb.core.DataSetCore
Removes duplicate gene rows in the data file and combines there values using the median
averageChildrenSigmas(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Forces children of a parent to both have the average of their standard deviations

B

backalg(double[], int[], int[], int[], int, DREM_Timeiohmm.Treenode, int, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Executes the backward portion of the baum-welch algorithm
bactual - Variable in class edu.cmu.cs.sb.core.GoAnnotations
boolean as to whether the profile enrichment should be actual size based (true) or expected size based (false)
badd0 - Variable in class edu.cmu.cs.sb.core.DataSetCore
True if a column of inital 0's should be added to the data file, false otherwise
BareBonesBrowserLaunch - Class in edu.cmu.cs.sb.chromviewer
Class to run webbrowser.
BareBonesBrowserLaunch() - Constructor for class edu.cmu.cs.sb.chromviewer.BareBonesBrowserLaunch
 
bcluster - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Whether the current order by ID are for a cluster of profiles (true) or profiles (false)
bcontoval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
boolean as to whether to include cellular component annotations
beforeInitialize() - Method in class edu.cmu.cs.sb.drem.DREMGui
Sets the screen size
beforeInitialize() - Method in class edu.cmu.cs.sb.stem.CompareGui
sets the size of the PFrame
beforeInitialize() - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Sets the screenSize
bfontoval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
boolean as to whether to include molecular function annotations
bfullrepeat - Variable in class edu.cmu.cs.sb.core.DataSetCore
If repeat data comes from distinct time series (true) that is a longitudal time series, otherwise it is false and each column of the same time point between data sets is interchangeable
binomialcumulative(double, double, double) - Static method in class edu.cmu.cs.sb.core.StatUtil
Computes the probability of seeing x or fewer successes in dN trials where the probability of a success is dp.
binomialtail(int, int, double) - Static method in class edu.cmu.cs.sb.core.StatUtil
Computes the probability of seeing more than x successes in N trials where the probability of a success is dp.
BiomartAccess - Class in edu.cmu.cs.sb.chromviewer
Class responsible for downloading gene locations from Biomart
BiomartAccess(String) - Constructor for class edu.cmu.cs.sb.chromviewer.BiomartAccess
Constructor, sets m_file to a File handle on fname
bmaxminval - Variable in class edu.cmu.cs.sb.core.DataSetCore
True if gene change threshold for filtering is based on the max-min difference False if the gene change threshold for filtering is based on the absolute difference
bpontoval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
boolean as to whether to include biological process annotations
brandomgoval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
boolean as to whether actual size based enrichment correction should be based on randomization (true) or Bonferroni false
bspotincluded - Variable in class edu.cmu.cs.sb.core.DataSetCore
True if the spot column was included in the data file
btakelog - Variable in class edu.cmu.cs.sb.core.DataSetCore
If the log-ratio taken (true); else data is already in log space (false)
buildEmptyTree(int, DREM_Timeiohmm.Treenode, double[], double[]) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Builds the initial tree which is just a single chain with mean and standard deviation for each node being the global mean and standard deviation at the time point
buildFilteredClassifier() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Uses DREM_NaiveBayes to build a classifier which predicts given the set of transcription factors predicted to regulate a gene whether it would appear filtered or not
buildRecDREM(DREM_Timeiohmm.Treenode, String[]) - Method in class edu.cmu.cs.sb.drem.DREM_GoAnnotations
 
buildset(String, String, String, String, String, String, int, double, double, int, int, int, String, boolean, Vector, boolean, boolean, boolean, String, String, String, boolean, boolean, boolean, boolean, boolean) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Returns a DREM_DataSet based on the provided input parameters
buildset(String, String, String, String, String, int, double, double, double, double, double, int, int, double, int, int, long, int, int, int, String, boolean, Vector, boolean, boolean, boolean, String, String, String, boolean, boolean, boolean, boolean, boolean, boolean, boolean, String, String, String) - Static method in class edu.cmu.cs.sb.stem.ST
Calls buildsetwithOrig but only returns the data set, not the pre-filtered gene list
buildsetwithOrig(String, String, String, String, String, int, double, double, double, double, double, int, int, double, int, int, long, int, int, int, String, boolean, Vector, boolean, boolean, boolean, String, String, String, boolean, boolean, boolean, boolean, boolean, boolean, boolean, String, String, String) - Static method in class edu.cmu.cs.sb.stem.ST
A driver method calling procedures to pre-process the data, and computer profile significance
buildxref(HashSet, HashMap) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Builds a cross reference mapping which as keys is alternative identifiers that map to a subset of genes in htgenes
buttonColor - Static variable in class edu.cmu.cs.sb.core.ListDialog
 

C

ChromEnrichmentTable - Class in edu.cmu.cs.sb.chromviewer
Table for an enrichment analysis on the set of genes assigned to each chromosome
ChromEnrichmentTable(JFrame, GenomeFileParser, int) - Constructor for class edu.cmu.cs.sb.chromviewer.ChromEnrichmentTable
Constructor - renders the enrichment table
ChromFrame - Class in edu.cmu.cs.sb.chromviewer
The class for the main interface window of the chromosome viewer
ChromFrame(String, GenomeFileParser, int) - Constructor for class edu.cmu.cs.sb.chromviewer.ChromFrame
Class constructor
ChromGeneAcceptTable - Class in edu.cmu.cs.sb.chromviewer
Table of the genes being displayed on the chromosome viewer
ChromGeneAcceptTable(JFrame, HashMap, Gene[], String) - Constructor for class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Constructor - renders the table
ChromGeneRejectTable - Class in edu.cmu.cs.sb.chromviewer
Class for table of genes that could not be displayed on the chromosome viewer
ChromGeneRejectTable(JFrame, HashSet, String) - Constructor for class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Class constructor - renders the table
chromosome - Variable in class edu.cmu.cs.sb.chromviewer.Gene
 
ChromRectangle - Class in edu.cmu.cs.sb.chromviewer
Class encapsulates a rectangle for a chromosome inherits some of the rectangle features from GeneRectangle
ChromRectangle(Gene, float, double, boolean, GenomeFileParser) - Constructor for class edu.cmu.cs.sb.chromviewer.ChromRectangle
Class constructor
chromView() - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Calls the chromosome viewer to draw and display gene on this table
chromViewInit(GenomeFileParser) - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Calls the chromosome viewer constructor
clearActiveGenes() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Clears empty genes
clearCounts(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Clears any prior assignments of genes to paths through the model
clearGenes() - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
Removes genes from the interface
clearGenes() - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle
Removes any genes in the rectangle
clone() - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Clones the classifier
clone() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet.ProfileRec
 
closeDefineWindows() - Method in class edu.cmu.cs.sb.stem.SortTable
Cloes the Define Gene Set window
closeSortWindows() - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Closes the windows to sort profiles or change interface options
closeToAllNeighbors(STEM_DataSet.ProfileRec, TreeSet) - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Returns true iff neighborProfile correlation with all profiles in tsNeighborhood is greater than or equal to dminclustdist
closeWindows() - Method in class edu.cmu.cs.sb.drem.DREMGui
Closes the frame windows
clusterArrayToString(ArrayList) - Static method in class edu.cmu.cs.sb.stem.ProfileGui
Static method that returns an array of profiles, a string with their profile IDs
clusterprofiles(boolean[], ArrayList, boolean) - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Method for clustering profiles
clusterscript(String, String, String, String, String, String, String, String, String, String, String, String, boolean, Vector, boolean, boolean, boolean, boolean, boolean, String, String, String, String, boolean, boolean, boolean, boolean, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_IO
A control method that handles the response for when the execute button on the interface is pressed including building the data set, running the DREM modeling procedure, and displaying the results
clusterscript(String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, int, String, String, boolean, Vector, boolean, boolean, boolean, boolean, boolean, boolean, String, String, String, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class edu.cmu.cs.sb.stem.ST
The method which drives the execution after the execute button is pressed getting the input and buiding the data sets
columnComparators - Variable in class edu.cmu.cs.sb.core.TableSorter
 
combineTrainAndTest() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Sets up the stored data so that the training data includes all data except any external held out validation data, meaning the data which might otherwise used for model selection is just for parameter learning
compactprofiles2(double, int) - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Implements the greedy algorithm to select a subset of the candidate model profiles based on dmaxcorrelationprofiles and nmaxprofiles
compare(Object, Object) - Method in class edu.cmu.cs.sb.core.GoAnnotations.GORankingComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.core.GoAnnotations.RecCompare
Compares first by dpvalue (lower comes first) and then by dcategoryselect (greater comes first)
compare(Object, Object) - Method in class edu.cmu.cs.sb.core.GoAnnotations.RecCompareBinom
Compares first by dpvaluebinom (lower comes first) and then by dcategoryselect (greater comes first)
compare(Object, Object) - Method in class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdremCompare
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.CompareGui.SigComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.CompareGui.SigRowComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.CompareGui.SupriseComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.CompareGui.SupriseRowComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.MAINGUI2.ProfileComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.MAINGUI2.ProfileexpComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.MAINGUI2.ProfileIDComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.MAINGUI2.ProfilenumComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.MAINGUI2.ProfilesigComparator
 
compare(Object, Object) - Method in class edu.cmu.cs.sb.stem.STEM_DataSet.Profilerecdistcomparator
 
CompareGui - Class in edu.cmu.cs.sb.stem
Class for the window that compares profiles
CompareGui(CompareInfo, PNode[], GenePlotPanel, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.CompareGui
Creates a comparison intersection interface backed on theCompareInfo
CompareGui.SigComparator - Class in edu.cmu.cs.sb.stem
Sorts individual profiles by p-value with reference profile in row, then profile ID
CompareGui.SigComparator() - Constructor for class edu.cmu.cs.sb.stem.CompareGui.SigComparator
 
CompareGui.SigRowComparator - Class in edu.cmu.cs.sb.stem
Sorts rows based on reference profile most significant intersection p-value, then profile ID
CompareGui.SigRowComparator() - Constructor for class edu.cmu.cs.sb.stem.CompareGui.SigRowComparator
 
CompareGui.SupriseComparator - Class in edu.cmu.cs.sb.stem
Sorts rows based on minimum correlation with reference profile, then profile ID
CompareGui.SupriseRowComparator - Class in edu.cmu.cs.sb.stem
Sorts rows based on minimum correlation with reference profile, then profile ID
CompareGui.SupriseRowComparator() - Constructor for class edu.cmu.cs.sb.stem.CompareGui.SupriseRowComparator
 
CompareInfo - Class in edu.cmu.cs.sb.stem
Class encapsulates information on the comparison of two STEM data sets focusing on identifying pairs of profiles with significant intersections between them.
CompareInfo(STEM_DataSet, String, String, String, Vector, boolean, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.CompareInfo
Launches a maingui for the comparison data and finds the significant pairs of intersections
componentHidden(ComponentEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui
Empty method
componentHidden(ComponentEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty method
componentMoved(ComponentEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui
Empty method
componentMoved(ComponentEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty method
componentResized(ComponentEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui
Calls drawmain
componentResized(ComponentEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty method
componentShown(ComponentEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui
Calls drawmain
componentShown(ComponentEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty method
computeaveragetally() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Computes the expected number of genes assigned to a profile based on a permutation test of time points
computeBestPvaluesClustersProfiles(STEM_DataSet) - Method in class edu.cmu.cs.sb.stem.STEM_GoAnnotations
Loads theRecIDpval and theClusterRecIDpval to have the p-values for the most enriched profiles and clusters for each category
computeDataStats(double[][], int[][], double[], double[]) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Computes the average and standard deviation expression level at each time point
computeG(int, boolean, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Updates the G parameters in the multi-class case bnew means the coefficient changed on the previous coordinate or first time if didn't change then can keep previous errors just update current coefficient bfirsttime means it is the first pass through the coeffienients
computeGbin(int, boolean, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Updates the value of the G matrix for the binary case bnew means the coefficient changed on the previous coordinate or first time If didn't change then can keep previous errors just update current coefficient bfirsttime means it is the first pass through the coefficients
computeminparentlevel(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Assigns to the nminparentlevel in all nodes the level of the most immediate ancestor with two or more children
computeNumLeaves(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Computes the number of paths to leaves accessible from each node in the tree pointed to by ptr
computeOrders(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Sorts the children of each node in treeptr and descendants based on OrderRecCompare
computeprofilestats() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Computes the average and standard deviation of the expression values of genes assigned to the same profile
computepval(int[][], double) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Computes the fraction of combinations for vals that could lead to a greater difference than ddiff
computePValues(HashMap, double) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns a record with GoResults, included corrected and uncorrected p-values for actual size enrichment for the category counts in htGoCounts
computePValues(HashMap, double, double) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns a record with GoResults, included corrected and uncorrected p-values for expected size enrichment for the category counts in htGoCounts
computePvaluesAssignments() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Computes the p-value for genes assigned to the same profile
computePValuesBase(HashMap, HashMap, double, int, boolean[]) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns a record with GoResults, included corrected and uncorrected p-values for actual size enrichment for the category counts in htGoCounts
computeStats(DREM_Timeiohmm.Treenode, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Computes association scores for the transcription factors overall on paths and on paths out of splits conditional on the set of genes going into the split
computevlogit(double[], int[], int[], int[], int, DREM_Timeiohmm.Treenode, int[]) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Recursively determines the best path through the model and its likelihood
containsTaxon(String, String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns true if an entry in sztaxonval is also an entry in szTaxon or after prepending a 'taxon:' szTaxon entries are delimited by pipes sztaxonval entries are delimited by semicolons, commas, and pipes
correlation(double[], double[]) - Static method in class edu.cmu.cs.sb.core.Util
Computes the correlation coefficient on the arrays xvalues and yvalues
correlation(double[], double[], int[]) - Static method in class edu.cmu.cs.sb.core.Util
Computes correlation coefficient between xvalues and yvalues only for those that have non-zero includex and includey values Returns 0 if no values are agree on for all data
correlation(double[], double[], int[], int[]) - Static method in class edu.cmu.cs.sb.core.Util
Computes correlation coefficient between xvalues and yvalues only for those that have non-zero includex and includey values Returns 0 if no values are agree on for all data
countNodes(DREM_Timeiohmm.Treenode, int) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Returns the number of nodes in the tree pointed by root for which its ncurrtime field does not equal the ncurrtime parameter
createImageIcon(String) - Static method in class edu.cmu.cs.sb.core.Util
Returns an ImageIcon, or null if the path was invalid.

D

dall - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoResults
The total number of genes in the base set
data - Variable in class edu.cmu.cs.sb.core.DataSetCore
The expression data, row are genes, columns are time points in experiments
data - Variable in class edu.cmu.cs.sb.core.ListDialog
 
data - Variable in class edu.cmu.cs.sb.core.TableModelSetST
A multi-dimensional array of data values
DataSetCore - Class in edu.cmu.cs.sb.core
The class encapsulates a set of gene expression data
DataSetCore() - Constructor for class edu.cmu.cs.sb.core.DataSetCore
Empty constructor
DataSetCore(DataSetCore) - Constructor for class edu.cmu.cs.sb.core.DataSetCore
Constructor copies each field
dataSetReader(String, int, double, double, boolean, boolean, boolean, boolean) - Method in class edu.cmu.cs.sb.core.DataSetCore
Reads in the datafile stored in szInputFile
DataTable - Class in edu.cmu.cs.sb.core
Class encapsulates a panel which is used to display the direct contents of a file in table format
DataTable(JFrame, String, boolean) - Constructor for class edu.cmu.cs.sb.core.DataTable
Constructor for the class szfile is the file containing the data to be displayed If bhorizontal is true then table resize mode is turned off
dcategoryall - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The number of genes in the category
dcategoryselect - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The number of genes in the category and in the set of interest
dclusterpval - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
cluster enrichment p-value
dcorrectedpvalue - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The corrected actual size based p-value
dcorrectedpvaluebinom - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The corrected expected size based p-value
DefineGeneSet - Class in edu.cmu.cs.sb.stem
Class encapsulates the window slecting which genes to select and unselect
DefineGeneSet(JFrame, MAINGUI2, GoAnnotations, ListSelectionModel, boolean) - Constructor for class edu.cmu.cs.sb.stem.DefineGeneSet
Constructor for class.
deleteMinPath(int[], int, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Deletes the specificed path from the model starting from ndesiredlevel
deletepath(int[], int, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Deletes a child from the specified path on a cloned version of the root node
DESCENDING - Static variable in class edu.cmu.cs.sb.core.TableSorter
 
dgenes - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Number of genes that are selected and belong to the profile
dgenescluster - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Number of genes that are selected and belong to the cluster
dgenestotal - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Number of genes that are selected
displayTempMap() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Displays the current temporary DREM model, from which a search is performed for an improved model
distortion(double[], double[], int[]) - Static method in class edu.cmu.cs.sb.core.Util
Returns the sum of the squared difference of xvalues and yvalues for non-zero include index values
distributionForInstance(int[], int) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Returns a probability distribution the classifier gives to each class for the provided instance
distributionForInstance(int[], int[], int) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Returns a probability distribution the classifier gives to each class for the provided instance
distributionForInstance(int[]) - Method in class edu.cmu.cs.sb.drem.DREM_NaiveBayes
Returns the probability of each class for the feature values in theInstance under the naive bayes models.
dmatch - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecCount
 
dmaxselect - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Number of genes that belong to the profile; max that could be selected in profile
dmaxselectcluster - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Number of genes that belong to the cluster; max that could be selected in cluster
dmaxselecttotal - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Total number of genes; max that could be selected
dmincorrelation - Variable in class edu.cmu.cs.sb.core.DataSetCore
Minimum average pairwise correlation a gene must have between full repeats if bfullrepeat is true
dminoverallpval - Variable in class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdrem
 
dminsplitpval - Variable in class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdrem
 
dnumexpected - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet.ProfileRec
 
dnumgenes - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet.ProfileRec
 
doubleToSz(double) - Static method in class edu.cmu.cs.sb.core.Util
Converts double into a formatted string representation
doubleToSz(double) - Static method in class edu.cmu.cs.sb.drem.DREMGui_EdgeTable
Converts the value of dval to a String that is displayed on the table
doubleToSz(double) - Static method in class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions
Converts a dobule value to a decimal formatted string
doubleToSz(double) - Static method in class edu.cmu.cs.sb.drem.DREMGui_KeyInputs
Converts a double value to a string as formatted as displayed on this interface
doubleToSz(double) - Static method in class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Converts double values to String values formatted as used in the table
doubleToSz(double) - Static method in class edu.cmu.cs.sb.stem.MAINGUI2
Converts a double value into a string
dpval - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
profile enrichment p-value
dpval - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecIDpval
 
dpvalbinom - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecIDpval2
 
dpvalhyper - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecIDpval2
 
dpvalue - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The uncorrected actual size based p-value
dpvalue - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet.ProfileRec
 
dpvaluebinom - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The uncorrected expected size based p-value
drawcomparemain() - Method in class edu.cmu.cs.sb.stem.CompareGui
Lays out the comparison panel
drawGenes(String[]) - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
Draws geneNames on the interface window
drawGenes(String[], Color) - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
Draws geneNames on the interface with the color "color"
drawintersectgo(Color) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Draws button for GO table for set of genes in a comparison intersection
drawmain() - Method in class edu.cmu.cs.sb.drem.DREMGui
Responsible for laying out the main interface window
drawmain() - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Renders the main interface window
drawNodes(DREM_Timeiohmm.Treenode, int, double, double, int, int, Color, Color, int, int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui
Draws nodes on the interface screen
DREM_DataSet - Class in edu.cmu.cs.sb.drem
Class extends DataSetCore which contains the underlying data and parameters of the methods with an instance of DREM_GoAnnotations
DREM_DataSet(DataSetCore, DREM_GoAnnotations) - Constructor for class edu.cmu.cs.sb.drem.DREM_DataSet
Constructor that does a simple copy the contents of theDataSetCore and tga
DREM_DataSet(String, int, double, double, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class edu.cmu.cs.sb.drem.DREM_DataSet
Constructor that takes input parameters and calls dataSetReader to read in the content of szInputFile
DREM_FastLogistic2 - Class in edu.cmu.cs.sb.drem
Class implements a logistic regression classifier trained with an L1 penalty.
DREM_FastLogistic2() - Constructor for class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Empty constructor
DREM_FastLogistic2(int[][], int[][], int[][], int[][], int[], int, double[], int) - Constructor for class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Constructor where the coefficients are given to the classifier
DREM_FastLogistic2(int[][], int[][], int[][], int[][], int[], double[], int, int) - Constructor for class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Constructor where the training weights of the instances are given
DREM_GoAnnotations - Class in edu.cmu.cs.sb.drem
Class encapsules the Gene Ontology annotations and gene set enrichment functions used by DREM
DREM_GoAnnotations.RecIDdrem - Class in edu.cmu.cs.sb.drem
A record for a GO category include ID, name, p-value based on a split, and a p-value overall
DREM_GoAnnotations.RecIDdrem(String, String, double, double) - Constructor for class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdrem
 
DREM_GoAnnotations.RecIDdremCompare - Class in edu.cmu.cs.sb.drem
Compares first by dpvalue (lower comes first) and then by dcategoryselect (greater comes first)
DREM_GoAnnotations.RecIDdremCompare() - Constructor for class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdremCompare
 
DREM_IO - Class in edu.cmu.cs.sb.drem
Class implementing the main input interface
DREM_IO() - Constructor for class edu.cmu.cs.sb.drem.DREM_IO
Class constructor - builds the input interface calls parseDefaults to get the initial settings from a default settings file if specified
DREM_IO.Downloadfile - Class in edu.cmu.cs.sb.drem
A runnable class used for controlling the downloading of files
DREM_IO.Progressdownload - Class in edu.cmu.cs.sb.drem
Runnable class used to display the download progress and also starts the download of a file
DREM_NaiveBayes - Class in edu.cmu.cs.sb.drem
Implements a naive bayes classifier This class is used for predicting whether a gene with a specified set of regulators will be filtered or not.
DREM_NaiveBayes(int[][], int[][], int, int[], int[], int) - Constructor for class edu.cmu.cs.sb.drem.DREM_NaiveBayes
Class constructor - builds the classifier
DREM_Timeiohmm - Class in edu.cmu.cs.sb.drem
This class implements the core methods for learning the DREM maps
DREM_Timeiohmm(DREM_DataSet, String, String, String, String, String, String, String, String, String, String, String, boolean, boolean, int, String, JLabel, JLabel, JLabel, JLabel, JLabel, JButton, boolean, boolean, double, double, double, int, double, double, JButton, String, String, boolean, String) - Constructor for class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Class constructor - provides the execution control on the method
DREMGui - Class in edu.cmu.cs.sb.drem
Class for the main interface window of a DREM regulatory map
DREMGui(DREM_Timeiohmm, DREM_Timeiohmm.Treenode, boolean, double, double, int, double, double, String, double) - Constructor for class edu.cmu.cs.sb.drem.DREMGui
Class constructor
DREMGui.SigInfoRec - Class in edu.cmu.cs.sb.drem
Record for information about significant transcription factors
DREMGui_DefineGeneSet - Class in edu.cmu.cs.sb.drem
Class for the window used to directly specify a subset of genes to select
DREMGui_DefineGeneSet(JFrame, GoAnnotations, DREMGui, DREM_Timeiohmm.Treenode) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Class constructor - builds the window
DREMGui_EdgeTable - Class in edu.cmu.cs.sb.drem
Class for a table that shows enrichment of TF targets along a path
DREMGui_EdgeTable(DREMGui, JFrame, DREM_Timeiohmm, DREM_Timeiohmm.Treenode, int, int, int, int, boolean) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_EdgeTable
Constructor - builds the table
DREMGui_FilterGOModel - Class in edu.cmu.cs.sb.drem
Class implements a table model, which is used for the define gene set table
DREMGui_FilterGOModel(Object[][], String[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Initializes the table model with the data, columnNames, and tga parameters
DREMGui_FilterStatic - Class in edu.cmu.cs.sb.drem
Class encapsulates window used to select a subset of genes based on the static transcription factors in the input to regulate the gene.
DREMGui_FilterStatic(JFrame, DREMGui, GoAnnotations, DREM_Timeiohmm.Treenode) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_FilterStatic
Class constructor - builds the interface window
DREMGui_FilterStaticModel - Class in edu.cmu.cs.sb.drem
Class implements a table model, which is used for selected genes based on static input
DREMGui_FilterStaticModel(Object[][], String[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Initializes the table model with the data, columnNames, and tga parameters
DREMGui_GeneTable - Class in edu.cmu.cs.sb.drem
Class encapsulates a gene table which is used to display the selected genes in DREM
DREMGui_GeneTable(JFrame, DREM_DataSet, DREM_Timeiohmm, int[][], int[][], int[][], int[][], String[], boolean[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Constructor builds the gene table interface
DREMGui_GOFilter - Class in edu.cmu.cs.sb.drem
Class encapsulates window used to select a subset of genes all belonging to the same GO category
DREMGui_GOFilter(JFrame, DREMGui, DREM_GoAnnotations.RecIDdrem[], DREM_Timeiohmm.Treenode) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_GOFilter
Class constructor - builds the panel window
DREMGui_GOGeneTable - Class in edu.cmu.cs.sb.drem
Class encapsulates a table of genes all assigned to the same GO category when clicking on a GO category in a GOTable
DREMGui_GOGeneTable(DREMGui, JFrame, DREM_DataSet, DREM_Timeiohmm, int[][], int[][], int[][], int[][], String[], String, boolean[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Class constructor - builds the table
DREMGui_GOSplitTable - Class in edu.cmu.cs.sb.drem
Encapsulates a table providing information on GO enrichments for the sets of genes on paths out of splits conditioned on the set of genes going into the split
DREMGui_GOSplitTable(DREMGui, JFrame, DREM_Timeiohmm, DREM_Timeiohmm.Treenode, int) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_GOSplitTable
Constructor - builds the table
DREMGui_GOTable - Class in edu.cmu.cs.sb.drem
Class that encapsulates a GO Enrichment table in DREM
DREMGui_GOTable(DREMGui, JFrame, DREM_DataSet, int[][], int[][], int[][], int[][], String[], boolean[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_GOTable
Constructor builds the GO enrichment table
DREMGui_ImageFilter - Class in edu.cmu.cs.sb.drem
Class used to specify the file filtering in the file chooser menu.
DREMGui_ImageFilter() - Constructor for class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
 
DREMGui_InterfaceOptions - Class in edu.cmu.cs.sb.drem
Class encapsulates the interface option window for the main interface
DREMGui_InterfaceOptions(JFrame, DREMGui) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions
Constructs the inteface option dialog window
DREMGui_KeyInputs - Class in edu.cmu.cs.sb.drem
Class encapsulates the window used to specify the criteria that determines transcription factor labels appear on the main interface
DREMGui_KeyInputs(JFrame, DREMGui) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_KeyInputs
Class constructor - builds interface window
DREMGui_Predict - Class in edu.cmu.cs.sb.drem
Class encapsulates a window to specify an input for each transcription factor, then displays a probability of transitioning to each hidden state
DREMGui_Predict(JFrame, DREMGui, DREM_Timeiohmm.Treenode) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_Predict
Constructs the prediction interface window
DREMGui_PredictModel - Class in edu.cmu.cs.sb.drem
Class implements a table model, which is used for the prediction interface
DREMGui_PredictModel(Object[][], String[]) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Initializes the table model with the data, columnNames, and tga parameters
DREMGui_SaveDREM - Class in edu.cmu.cs.sb.drem
Class for window to specify to save the current DREM main interface as an image
DREMGui_SaveDREM(DREMGui, JFrame) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_SaveDREM
Class constructor builds the panel window
DREMGui_SaveModel - Class in edu.cmu.cs.sb.drem
Class to encapsulate window used to specify a file to save a DREM model
DREMGui_SaveModel(DREM_Timeiohmm, DREM_Timeiohmm.Treenode, JFrame, DREMGui) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_SaveModel
Class constructor
DREMGui_SplitTable - Class in edu.cmu.cs.sb.drem
Class encapsulating a table showing enrichment of gene targets of transcription factors out of splits
DREMGui_SplitTable(DREMGui, JFrame, DREM_Timeiohmm, DREM_Timeiohmm.Treenode, int) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Constructor for a table giving information on a split when there are two paths out of the split
DREMGui_SplitTable(DREMGui, JFrame, DREM_Timeiohmm, DREM_Timeiohmm.Treenode, int, int, int) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Constructor for a table giving information on a split when there are three or more paths out of the split
DREMGui_StaticSummaryTable - Class in edu.cmu.cs.sb.drem
Class for a table summarizing the TF-gene enrichments for a selected set of gene This is the table that comes up when pressing the TF summary button
DREMGui_StaticSummaryTable(JFrame, DREM_DataSet, DREM_Timeiohmm, int[][], int[][], String[], boolean[], int) - Constructor for class edu.cmu.cs.sb.drem.DREMGui_StaticSummaryTable
Constructor builds the table
DSAME - Static variable in class edu.cmu.cs.sb.stem.STEM_DataSet
 
dsamplemins - Variable in class edu.cmu.cs.sb.core.DataSetCore
The time points at which the expression data was sampled
dselect - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoResults
The number of genes in the set being analyzed
dthresholdvalue - Variable in class edu.cmu.cs.sb.core.DataSetCore
The threshold value for required change
dtotal - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecCount
 

E

edu.cmu.cs.sb.chromviewer - package edu.cmu.cs.sb.chromviewer
 
edu.cmu.cs.sb.core - package edu.cmu.cs.sb.core
 
edu.cmu.cs.sb.drem - package edu.cmu.cs.sb.drem
 
edu.cmu.cs.sb.stem - package edu.cmu.cs.sb.stem
 
EMPTY_DIRECTIVE - Static variable in class edu.cmu.cs.sb.core.TableSorter
 
end - Variable in class edu.cmu.cs.sb.chromviewer.Gene
 
enrichedToSz(double) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Converts the number of genes enriched as a double to a string representation
equals(Object) - Method in class edu.cmu.cs.sb.chromviewer.Gene
True if both objects are equal with all the same field values
errorcheck(DREM_DataSet, DREM_DataSet) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Checks if the two data sets have the same number of rows, time points, and the gene name matches.
errorcheck(String[], String[], int, int) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Checks if origcols and nrepeat cols are the same value, the length of origgenes and repeatgenes is the same, and the gene names are the same
errorcheck(STEM_DataSet, STEM_DataSet) - Static method in class edu.cmu.cs.sb.stem.ST
Makes sure repeat data sets agree with each other on the number of rows, columns, and the name of the genes
errorcheck(String[], String[], int, int) - Static method in class edu.cmu.cs.sb.stem.ST
Makes sure repeat data sets agree with each other on the number of columns and the name of the genes
euclidean(double[], double[], int[]) - Static method in class edu.cmu.cs.sb.core.Util
Returns the euclidean distance between xvalues and yvalues for those include values that are non-zero.
executeCountQuery(String) - Method in class edu.cmu.cs.sb.chromviewer.BiomartAccess
Executes the BioMart query in xmlMessage that counts the number of records satisfying query.
executeQuery(BufferedOutputStream, String, int[], int, Object) - Method in class edu.cmu.cs.sb.chromviewer.BiomartAccess
ExecuteQuery.
extragenes - Variable in class edu.cmu.cs.sb.core.GoAnnotations
List of extra gene ids to add to the base set from the szextraval file i^th index of extra genes should correspond to i^th index of extraprobes
extraprobes - Variable in class edu.cmu.cs.sb.core.GoAnnotations
List of extra probe ids to add to the base set from the szextraval file

F

filterdistprofiles(DataSetCore, DataSetCore[]) - Method in class edu.cmu.cs.sb.core.DataSetCore
Computes the average pairwise correlation between gene repeats stores it in sortedcorrvals.
filterDuplicates() - Method in class edu.cmu.cs.sb.core.DataSetCore
Removes those rows which are the duplicate of another row.
FilteredTable - Class in edu.cmu.cs.sb.stem
Class for the table of genes that have been filtered
FilteredTable(JFrame, STEM_DataSet) - Constructor for class edu.cmu.cs.sb.stem.FilteredTable
Constructor that builds the table
filtergenesgeneral(boolean[], int, boolean) - Method in class edu.cmu.cs.sb.core.DataSetCore
Filters those rows which do not have a true in keepgene nkeep is the number of true rows in keepgene If bstore is true and gene is filtered then we stroe the gene and proble list for it in htFiltered Returns a new DataSetCore object with those rows filtered
filtergenesthreshold1point() - Method in class edu.cmu.cs.sb.core.DataSetCore
Filters those genes with expression below dthresholdvalue
filtergenesthreshold2() - Method in class edu.cmu.cs.sb.core.DataSetCore
If bmaxminval is true, then filter those genes for which the difference between the max and min value is less than dthresholdvalue If bmaxminval if false, then filter those genes for which the absolute expression change is less than dmaxval
filterMissing() - Method in class edu.cmu.cs.sb.core.DataSetCore
Filter those rows which have nmaxmissing or more missing values or are missing the first time point value
filterMissing1point() - Method in class edu.cmu.cs.sb.core.DataSetCore
Filters those rows that have a missing value at the first time point
findbestgroupassignments() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Finds the best profile which matches each gene
findmins(HashMap, HashMap, DREM_Timeiohmm.Treenode, String[], HashMap) - Method in class edu.cmu.cs.sb.drem.DREM_GoAnnotations
Determines the minimum overall and split p-values for each
findnodesAtLevel(DREM_Timeiohmm.Treenode, int, HashSet) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Returns true iff all nodes at nleveltogo only have one path to the leaves Stores in hsLevel all nodes at nleveltogo is 0
findsigcompare() - Method in class edu.cmu.cs.sb.stem.CompareInfo
Finds significant pairs of profiles from the two data sets interms of an intersection exceeding nminnumgenes and p-value less than dmaxpval
FLOATERROR - Static variable in class edu.cmu.cs.sb.stem.STEM_DataSet
 
forwardalg(double[], int[], int[], int[], int, double, DREM_Timeiohmm.Treenode, int, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Executes the forward algorithm portion of the baum-welch algorithm

G

Gene - Class in edu.cmu.cs.sb.chromviewer
Encapsulates information about a gene
Gene() - Constructor for class edu.cmu.cs.sb.chromviewer.Gene
 
geneIsOfType(String, String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns true if the gene ID szID is of type szCategory any sub entry or the entire string could match where entries are delimited by semicolons, pipes, or commas
genenames - Variable in class edu.cmu.cs.sb.core.DataSetCore
The list of gene names for the current data set
GenePlotPanel - Class in edu.cmu.cs.sb.stem
Class controls the panel for displaying interface options
GenePlotPanel(JFrame, MAINGUI2, boolean) - Constructor for class edu.cmu.cs.sb.stem.GenePlotPanel
Constructor for the interface options
GeneRectangle - Class in edu.cmu.cs.sb.chromviewer
Draws gene rectangles on the main chromosome interface
GeneRectangle(Gene, String, float, double, boolean, GenomeFileParser) - Constructor for class edu.cmu.cs.sb.chromviewer.GeneRectangle
Rectangle constructor
GeneRectangle.GeneMouseOverHandler - Class in edu.cmu.cs.sb.chromviewer
Handles various mouse events on the interface
GeneRectangle.GeneMouseOverHandler() - Constructor for class edu.cmu.cs.sb.chromviewer.GeneRectangle.GeneMouseOverHandler
 
generepeatspottimedata - Variable in class edu.cmu.cs.sb.core.DataSetCore
Present/missing data for several data sets First dimension is gene Second dimension is repeat Third dimension is spot Fourth dimension is expression value (in log ratio form against time zero)
generepeatspottimepma - Variable in class edu.cmu.cs.sb.core.DataSetCore
Present/missing data for several data sets First dimension is gene Second dimension is repeat Third dimension is spot Fourth dimension is present/missing value
genespottimedata - Variable in class edu.cmu.cs.sb.core.DataSetCore
Present/missing data for one data set First dimension is gene Second dimension is spot Third is expression value (in log ratio form against time zero)
genespottimepma - Variable in class edu.cmu.cs.sb.core.DataSetCore
Present/missing data for one data set First dimension is gene Second dimension is spot Third is present/missing value
GeneTable - Class in edu.cmu.cs.sb.stem
Class for a table of genes assigned to a profile or cluster
GeneTable(JFrame, STEM_DataSet, int, String, boolean, HashSet, String, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.GeneTable
Constructor to display genes associated with a single profile or cluster
GeneTable(JFrame, STEM_DataSet, ArrayList, String, boolean, HashSet, String, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.GeneTable
Constructor to display genes associated with a set of profiles
geneTableHelper(STEM_DataSet, String, boolean, HashSet) - Method in class edu.cmu.cs.sb.stem.GeneTable
Builds the gene table interface
GenomeFileParser - Class in edu.cmu.cs.sb.chromviewer
Class responsible for parsing and storing a file of the location of chromosome location of genes
GenomeFileParser() - Constructor for class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Empty constructor
GenomeFileParser(String, String, String[], ArrayList, boolean, int) - Constructor for class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Constructor that attempts to load
genomeParser - Variable in class edu.cmu.cs.sb.chromviewer.ChromFrame
 
getCategory(ArrayList, String[], ArrayList[], boolean, HashSet) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the GO results for actual size based enrichment for a set where the indicies of the set of genes in the set is ids If bqueryset is true, then only genes also in the query set will be used If htinames is non-null, then only genes also in htinames will be used
getCategory(String[], boolean[], boolean[]) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the GO results for actual size based enrichment for a set where the set of genes in the set are those with positive weight
getCategory(String[], double[]) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the GO results for actual size based enrichment for a set where the set of genes in the set are those with positive weight
getCategory(ArrayList, String[], ArrayList[], boolean, HashSet, double) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the GO results for expected size based enrichment for a set where the indicies of the set of genes in the set is ids If dexpected is <0, returns an actual size based enrichment If bqueryset is true, then only genes also in the query set will be used If htinames is non-null, then only genes also in htinames will be used
getCategory(ArrayList, ArrayList[], String[], ArrayList[], boolean, HashSet) - Method in class edu.cmu.cs.sb.stem.STEM_GoAnnotations
Used to get the GO results for a cluster of profiles the id of each profile in the cluster is listed in profileList an array list in ids has all the indicies in genenames assigned to the profile If bqueryset is true, then only genes also in the query set will be used If htinames is non-null, then only genes also in htinames will be used
getChromArray() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Variable accessor method
getChromLenMax() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Variable accessor method
getChroms() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Variable accessor method
getColumnClass(int) - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns the Class type of column c
getColumnClass(int) - Method in class edu.cmu.cs.sb.core.TableModelST
Returns the Class type of column c
getColumnClass(int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getColumnClass(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns the Class type of column c
getColumnClass(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns the Class type of column c
getColumnClass(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns the Class type of column c
getColumnCount() - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns the number of columns
getColumnCount() - Method in class edu.cmu.cs.sb.core.TableModelST
Returns the number of columns
getColumnCount() - Method in class edu.cmu.cs.sb.core.TableSorter
 
getColumnCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns the number of columns
getColumnCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns the number of columns
getColumnCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns the number of columns
getColumnName(int) - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns the column name of ncol
getColumnName(int) - Method in class edu.cmu.cs.sb.core.TableModelST
Returns the column name of ncol
getColumnName(int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getColumnName(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns the column name of ncol
getColumnName(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns the column name of ncol
getColumnName(int) - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns the column name of ncol
getComparator(int) - Method in class edu.cmu.cs.sb.chromviewer.TableSorterRoman
Access method on a comparator
getComparator(int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getDescription() - Method in class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
Returns szdesc
getExtension(File) - Static method in class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
Returns the extension of the file
getFile(String, String, int) - Method in class edu.cmu.cs.sb.drem.DREM_IO
Download the data at the location of szURL into a file szoutfile ntype is used for updating the download progress percentages
getFile(String, String, int) - Method in class edu.cmu.cs.sb.stem.ST
Responsible for downloading the file.
getgocategories(String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the HashSet of gocategories for szannotation If such a set does not exist creates it
getHeaderRendererIcon(int, int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getImageURL(String) - Static method in class edu.cmu.cs.sb.core.Util
Returns an URL for the path, or null if the path was invalid.
getLevel(String, HashSet) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns the level of the GO ID of szTerm level is defined in terms of maximum length to a root
getmedian(double[], int) - Static method in class edu.cmu.cs.sb.core.Util
Returns the median value in vals in indicies between 0 and nvalindex-1
getName() - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle
Returns the chromosome corresponding to the gene in the rectangle
getProfileRankings(ArrayList, ArrayList[], String[], ArrayList[], double[]) - Method in class edu.cmu.cs.sb.stem.STEM_GoAnnotations
Puts in tpgr a sorted ranking of profiles based on the current sort by seelctions
getRowCount() - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns the number of rows
getRowCount() - Method in class edu.cmu.cs.sb.core.TableModelST
Returns the number of rows
getRowCount() - Method in class edu.cmu.cs.sb.core.TableSorter
 
getRowCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns the number of rows
getRowCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns the number of rows
getRowCount() - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns the number of rows
getSortingStatus(int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getSpecies() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Variable accessor method
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.cmu.cs.sb.core.MultiLineHeaderRenderer
Renders the data in value
getTableHeader() - Method in class edu.cmu.cs.sb.core.TableSorter
Returns the tableHeader
getTableModel() - Method in class edu.cmu.cs.sb.core.TableSorter
Returns the tableModel
getValidAttributes(String) - Method in class edu.cmu.cs.sb.chromviewer.BiomartAccess
Gets a HashSet of valid attributes for the gene location
getValueAt(int, int) - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns the value in the table in row nrow and column ncol
getValueAt(int, int) - Method in class edu.cmu.cs.sb.core.TableModelST
Returns the value in the table in row nrow and column ncol
getValueAt(int, int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
getValueAt(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns the value in the table in row nrow and column ncol
getValueAt(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns the value in the table in row nrow and column ncol
getValueAt(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns the value in the table in row nrow and column ncol
goAll - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Array of hash sets of GO categories of each unique gene
GoAnnotations - Class in edu.cmu.cs.sb.core
The class encapsulates the data and functions related to the Gene Ontology and gene set enrichment analysis
GoAnnotations(String, String, String, String, String, String[], String[], int, int, int, String, String, boolean, String, String, boolean, boolean, boolean, boolean) - Constructor for class edu.cmu.cs.sb.core.GoAnnotations
Constructs a GoAnnotation object.
GoAnnotations.GORankingComparator - Class in edu.cmu.cs.sb.core
Compartor for two profile ranking records
GoAnnotations.GORankingComparator() - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.GORankingComparator
 
GoAnnotations.GoRec - Class in edu.cmu.cs.sb.core
Stores GO enrichment results for one category
GoAnnotations.GoRec(double, double, double, String, String) - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.GoRec
Constructor without expected size based p-value
GoAnnotations.GoResults - Class in edu.cmu.cs.sb.core
Encapsulates a set of GO enrichment results
GoAnnotations.GoResults(double, double, GoAnnotations.GoRec[]) - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.GoResults
Constructor for GoResults
GoAnnotations.ProfileGORankingRec - Class in edu.cmu.cs.sb.core
Stores info about a profile's ranking according to the current order by criteria
GoAnnotations.ProfileGORankingRec(int, int, double, double, double, double, double, double, double, double) - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
 
GoAnnotations.Rec - Class in edu.cmu.cs.sb.core
Rec is a Gene Ontology hierarchy record a GO ID will map to the record A record contains a name and a set of parent records
GoAnnotations.Rec(HashSet, String) - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.Rec
Initializes parents and sztermName
GoAnnotations.RecCompare - Class in edu.cmu.cs.sb.core
Comparator for GoRec based on actual size p-value
GoAnnotations.RecCompare() - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.RecCompare
 
GoAnnotations.RecCompareBinom - Class in edu.cmu.cs.sb.core
Comparator for GoRec based on expected size p-value
GoAnnotations.RecCompareBinom() - Constructor for class edu.cmu.cs.sb.core.GoAnnotations.RecCompareBinom
 
GoAnnotations.RecCount - Class in edu.cmu.cs.sb.core
A count of the total count of the number of genes in a set (dtotal) and the number selected based on the ordering criteria (dmatch)
GoAnnotations.RecIDpval - Class in edu.cmu.cs.sb.core
A record containing a GO ID and a p-val
GoAnnotations.RecIDpval2 - Class in edu.cmu.cs.sb.core
A record containing a GO ID and an actual and an expected size p-val
GOGeneTable - Class in edu.cmu.cs.sb.stem
Class responsible for displaying the genes indicated to be assigned to a GO category in a gene table
GOGeneTable(JFrame, STEM_DataSet, String, String, int, String, ArrayList, boolean, HashSet, String, boolean, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.GOGeneTable
Class constructor renders the table
goRecArray - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoResults
An array of GO enrichment records
GOTable - Class in edu.cmu.cs.sb.stem
Encapsulates a table for a GO enrichment analysis where enrichment is based on the actual number of genes assigned to a profile.
GOTable(JFrame, STEM_DataSet, int, ArrayList, boolean, HashSet, String, boolean, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.GOTable
Constructor which renders the table
GOTableExpected - Class in edu.cmu.cs.sb.stem
Encapsulates a Gene Ontology enrichment analysis where the enrichment calculation is based on the expected number of genes to the profile
GOTableExpected(JFrame, STEM_DataSet, int, ArrayList, boolean, HashSet, String, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.GOTableExpected
Constructor for the GO table, renders the table

H

handlechromval() - Method in class edu.cmu.cs.sb.stem.ST
Responds to changes in the gene location field on the input interface
handleclusteringmethod() - Method in class edu.cmu.cs.sb.stem.ST
Responds to changes in the desired clustering method on the interface
handlendbval() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Updates the interface and internal values for the GO cross reference input
handlendbval() - Method in class edu.cmu.cs.sb.stem.ST
Handles changes to changes in GO or cross-reference data sources
handlenxrefval() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Updates the interface and internal values for the GO cross reference input
handlenxrefval() - Method in class edu.cmu.cs.sb.stem.ST
Responds to changes in the gene annotation cross reference field on the main interface
handlestaticsource() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Updates the interface and internal values for the static TF-gene input
hashCode() - Method in class edu.cmu.cs.sb.chromviewer.Gene
Converts the gene information to a unique integer hash code
hashtoList1(HashMap, GoAnnotations.RecIDpval[]) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Iterates over hIDpval storing its contents in currRecIDA, and then sorting currRecIDA.
hashtoList2(HashMap, GoAnnotations.RecIDpval2[]) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Iterates over hIDpval storing its contents in currRecIDA, and then sorting currRecIDA.
hasMerge(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Returns true iff treeptr or a descendent has two or more parents
hidelabels() - Method in class edu.cmu.cs.sb.drem.DREMGui
Hides all annotation labels
htAlt - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps alternative IDs to the ID used in the hierarchy
htAncestors - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps a GO ID to it set of ancestor IDs
htbinom - Static variable in class edu.cmu.cs.sb.core.StatUtil
this hashtable caches previously computed binomial coefficient values so they do not need to be recomputed
htFiltered - Variable in class edu.cmu.cs.sb.core.DataSetCore
Contains genes filtered.
htFullCount - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps a category to the total number of genes annotated as belonging to the category.
htGeneNames - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps every gene name to a boolean as to whether or not it is selected in the define gene set menu.
htGO - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps go category ids to their records contains their name and parents
htGoLabels - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps a gene ID to a list of go categories for which it is annotated.
htIDCategory - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Maps ids in the categoryID file to category names
hypergeometric(int, int, int, int) - Static method in class edu.cmu.cs.sb.core.StatUtil
Returns the probability of seeing x of type A, when there nA objects of type A nB objects of type B, and nm objects total drawn
hypergeometriccumulativex(int, int, int, int) - Static method in class edu.cmu.cs.sb.core.StatUtil
Returns the probability of seeing x or fewer objects of type A, when there are nA objects of type A nB objects of type B, and nm objects total drawn
hypergeometrictail(int, int, int, int) - Static method in class edu.cmu.cs.sb.core.StatUtil
Returns the probability of seeing more than x objects of type A, when there are nA objects of type A nB objects of type B, and nm objects total drawn This can be used to compute a more accurate p-values than a 1-cumulative probability calculation

I

incrementSelectData(ArrayList, String[], ArrayList[], boolean, String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Counts the total weight of assignments in assignedgenes.
indivButton - Variable in class edu.cmu.cs.sb.core.ListDialog
 
init() - Method in class edu.cmu.cs.sb.stem.ProfileGui
Initializes the colors
initAE(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Initializes all the fields that will be used by instanceAE
initAEV(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Initializes all the fields that will be used by instanceAEV
initialize() - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
Empty initialize method
initialize() - Method in class edu.cmu.cs.sb.drem.DREMGui
calls drawmain
initialize() - Method in class edu.cmu.cs.sb.stem.CompareGui
Simply calls drawcomparemain
initialize() - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Initializes the interface
initializeDefaults() - Static method in class edu.cmu.cs.sb.stem.ST
Initializes the default settings of all the variables
instanceAE(DREM_Timeiohmm.Treenode, int, double[], int[], int[], double, int) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Combines the results of the forward and backward algorithm to obtain the probability of each gene going through each state when using baum-welch training
instanceAEV(DREM_Timeiohmm.Treenode, double[], int[], int[], int[], double, int) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Combines the results of the forward and backward algorithm to obtain the probability of each gene going through each state when using viterbi training
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.core.TableModelSetST
Returns true if ColumnIndex is 1, otherwise returns false
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.core.TableModelST
Always returns false, no cell is editable under this model
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Returns true if ColumnIndex is 1, otherwise returns false
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Returns true if ColumnIndex is >=1, otherwise returns false
isCellEditable(int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Returns true if ColumnIndex is 1, otherwise returns false
isOrder(String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns true if the profiles are sorted based on a GO category or user defined gene set and szGene is part of that category or gene set.
isSorting() - Method in class edu.cmu.cs.sb.core.TableSorter
Returns true iff the sortingColumns size is not 0
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Responds to changes in whether enrichment labels should be based on splits or overall
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStatic
Responds to a change in the selection of the radio button
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOFilter
Responds to changes in the radio buttons
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions
Responds to item changes on the interface window
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_KeyInputs
Responds to changes with the radio buttons
itemStateChanged(ItemEvent) - Method in class edu.cmu.cs.sb.stem.GenePlotPanel
Responds to itemStateChanged events

K

kmeans() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Implements the k-means clustering method

L

labelsForID(String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Given a string of delimited IDs, returns any categories which map to an entry of the string or the whole string
layoutChildren() - Method in class edu.cmu.cs.sb.chromviewer.ChromRectangle
Layouts out the genes on the rectangle
levelGO() - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns a HashSet of GO IDs with level below nmingolevel Removes those IDs from htGO
LEXICAL_COMPARATOR - Static variable in class edu.cmu.cs.sb.core.TableSorter
Used to compare two table entries
LEXICALROMAN_COMPARATOR - Static variable in class edu.cmu.cs.sb.chromviewer.TableSorterRoman
 
ListDialog - Class in edu.cmu.cs.sb.core
 
ListDialog(JFrame, Vector, boolean, JButton, Color, Color, JFileChooser) - Constructor for class edu.cmu.cs.sb.core.ListDialog
Constructors the Repeat interface
loadBinding(String, int[], int[], int) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Stores into htbinding the mapping of the gene szid to its non-zero TF-gene interactions given by nonzeroindex and nonzerovals
loadID(String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Adds genes to htGeneNames, updates the numtotalgenes count htFullCounts, and adds to algoAll
loadIDbase(String, HashMap, ArrayList) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Updates htBase for all categories of baseGene.
loadIDCategory() - Method in class edu.cmu.cs.sb.core.GoAnnotations
Maps ids to category names for non-official go categories specified in the file szcategoryIDval in the htIDCategory hash map.
loadTable(ArrayList) - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Adds to the table the genes that should be displayed on the table
logbinomcoeff(int, int) - Static method in class edu.cmu.cs.sb.core.StatUtil
Returns the log of the binomial coefficient N choose ni
logratio2() - Method in class edu.cmu.cs.sb.core.DataSetCore
Converts data into log-ratio versus the first time point.

M

main(String[]) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
The main method which when executed will have the input interface created
main(String[]) - Static method in class edu.cmu.cs.sb.stem.ST
The main method which launches STEM
MAINGUI2 - Class in edu.cmu.cs.sb.stem
The class for the overview interface window that shows all the profiles or k-means clusters
MAINGUI2(STEM_DataSet) - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2
Class constructor
MAINGUI2.ProfileComparator - Class in edu.cmu.cs.sb.stem
The default profile comparison.
MAINGUI2.ProfileComparator() - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2.ProfileComparator
 
MAINGUI2.ProfileexpComparator - Class in edu.cmu.cs.sb.stem
Compares profiles based on expectected number of genes assigned then by ID
MAINGUI2.ProfileexpComparator() - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2.ProfileexpComparator
 
MAINGUI2.ProfileIDComparator - Class in edu.cmu.cs.sb.stem
Compares profiles based on profile IDs
MAINGUI2.ProfileIDComparator() - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2.ProfileIDComparator
 
MAINGUI2.ProfilenumComparator - Class in edu.cmu.cs.sb.stem
Compares profiles based on number of genes assigned then by ID
MAINGUI2.ProfilenumComparator() - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2.ProfilenumComparator
 
MAINGUI2.ProfilesigComparator - Class in edu.cmu.cs.sb.stem
Compares profiles based on the p-valu signficance, then based on number of genes assigned, number expected, and then ID
MAINGUI2.ProfilesigComparator() - Constructor for class edu.cmu.cs.sb.stem.MAINGUI2.ProfilesigComparator
 
MainTable - Class in edu.cmu.cs.sb.stem
Class which contains table for all genes that were not filtered.
MainTable(JFrame, STEM_DataSet, GenePlotPanel, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.MainTable
Constructor to build a new main table
makeAdditionalSearchPanel() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Makes the panel showing the model selection options
makeAnnotationPanel() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Makes the GO annotation options panel
makeAnnotationPanel() - Method in class edu.cmu.cs.sb.stem.ST
Renders the option panel about gene annotations
makeClusteringPanel() - Method in class edu.cmu.cs.sb.stem.ST
Makes panel of options for the clustering model profiles
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class edu.cmu.cs.sb.core.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeCompareDialog() - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Renders the dialog to specify a comparison data set
makeComparePanel(Container) - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Renders the panel within the dialog to compare data sets
makeFilterPanel() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Makes the option panel on the input interface controlling gene filtering.
makeFilterPanel() - Method in class edu.cmu.cs.sb.stem.ST
Makes panel of gene filtering options
makeGOAnalysisPanel() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Makes the GO analysis options panel
makeGOAnalysisPanel() - Method in class edu.cmu.cs.sb.stem.ST
Render the GO Analysis options panels
makeGrid(Container, int, int, int, int, int, int) - Static method in class edu.cmu.cs.sb.core.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeHelpDialog(Component) - Method in class edu.cmu.cs.sb.drem.DREM_IO
Renders a help dialog based on the specific help button pressed
makeHelpDialog(Component) - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Renders the window to provide help information
makeHelpDialog(Component) - Method in class edu.cmu.cs.sb.stem.ST
Renders help information for the various help buttons on the interface
makeModelPanel() - Method in class edu.cmu.cs.sb.stem.ST
Makes panel of options related to the selection and significance of model profiles
makeOptionsDialog() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Renders the tabbed set of option window panes
makeOptionsDialog() - Method in class edu.cmu.cs.sb.stem.ST
Manages the rendering of the set of option tabbed panels
makeSearchPanel() - Method in class edu.cmu.cs.sb.drem.DREM_IO
Makes the option panel on the input interface controlling the search options
makeTFindex(int[][], int[][], int[][], int[][]) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Generates pvalTF and pvalTFindex based on pval and pvalindex so that the rows correspond to each TF and each entry in a row pvalTFindex corresponds to an index of a gene the TF regulates and the corresponding entry in pvalTF corresponds to the interaction value
makewindow() - Method in class edu.cmu.cs.sb.stem.DefineGeneSet
Controls the interface window for defining gene sets
mergeDataSets(DataSetCore[]) - Method in class edu.cmu.cs.sb.core.DataSetCore
Given an array of otherDataSets, merges it with the current data set by storing in data the median of the values.
mGeneAlias - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 
mGeneInfo - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 
mHorizontalOrientation - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 
mInputListener - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 
mLeftToRight - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 
modelIndex(int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
modelprofilestats(double[], double[], double[]) - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Computes sum and variance statistics on model profiles
mouseClicked(PInputEvent) - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle.GeneMouseOverHandler
 
mouseClicked(MouseEvent) - Method in class edu.cmu.cs.sb.core.TableSorter.MouseHandler
 
mouseClicked(MouseEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Responds to mouse clicked events
mouseEntered(PInputEvent) - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle.GeneMouseOverHandler
 
mouseEntered(MouseEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty constructor method
mouseExited(PInputEvent) - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle.GeneMouseOverHandler
 
mouseExited(MouseEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty constructor method
mouseListener - Variable in class edu.cmu.cs.sb.core.TableSorter
 
mouseMoved(PInputEvent) - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle.GeneMouseOverHandler
 
mousePressed(MouseEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty constructor method
mouseReleased(MouseEvent) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Empty constructor method
MultiLineHeaderRenderer - Class in edu.cmu.cs.sb.core
Class implements multiple lines in a table header Code based on http://www.codeguru.com/java/articles/126.shtml
MultiLineHeaderRenderer(TableSorter) - Constructor for class edu.cmu.cs.sb.core.MultiLineHeaderRenderer
Initializes the TableSorter object to the header.
mWidthScale - Variable in class edu.cmu.cs.sb.chromviewer.GeneRectangle
 

N

namechrom - Variable in class edu.cmu.cs.sb.chromviewer.Gene
 
ncluster - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
Cluster profile belongs to, non-significant profiles have the greatest cluster value
nextw(int, boolean, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
For the multi-class case updates the value of dcoeff[nel]
nextwbin(int, boolean, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
For the binary case updates the value of dcoeff[nel]
nGeneSet - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Stores a count of the number
nlegalgo - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The number of GO Categories
nmaxmissing - Variable in class edu.cmu.cs.sb.core.DataSetCore
The maximum number of missing values to prevent a gene from being filtered.
nmaxsize - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Contains the maximum number of genes in any category
nmingo - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The minimum number of genes in a set and belonging to a category for the category to be included in a GO analysis table
nmingolevel - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The minimum GO level to include inthe analysis, where level 1 is the molecular function, biological process, and cellular location level
normaldensity(double, double, double) - Static method in class edu.cmu.cs.sb.core.StatUtil
computes the value of f(x) where f is a density for a normal distribution with mean dmu and standard deviation dsigma.
NOT_SORTED - Static variable in class edu.cmu.cs.sb.core.TableSorter
 
nprofile - Variable in class edu.cmu.cs.sb.core.GoAnnotations.ProfileGORankingRec
profile id
nprofileindex - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet.ProfileRec
 
nsamplespval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The number a samples to use when the multiple hypothesis correction is based on randomization.
numcategory - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Contains the total number of GO categories
numcols - Variable in class edu.cmu.cs.sb.core.DataSetCore
Number of columns in the data matrix.
numrows - Variable in class edu.cmu.cs.sb.core.DataSetCore
Number of rows in the data matrix.
numtotalgenes - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The total number of non-duplicate genes on the array

O

openURL(String) - Static method in class edu.cmu.cs.sb.chromviewer.BareBonesBrowserLaunch
Opens browser pointed to url
otherInputFiles - Variable in class edu.cmu.cs.sb.core.DataSetCore
The names of the other repeat files

P

p(int, int) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Computes the probability of the item in nrow is of class nindicator
paint(Graphics) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Renders the interface by getting the interface option settings and then calling plotgenevalues
parents - Variable in class edu.cmu.cs.sb.core.GoAnnotations.Rec
A set of parents in the hierarchy
parseDefaults() - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Assigns the initial settings of the parameters based on the contents of szDefaultFile
parseDefaults(String) - Static method in class edu.cmu.cs.sb.stem.ST
Parse the contents of a defaults file
parsedOK() - Method in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
Variable accessor method
plotgenevalues(Graphics2D, double, double, double, double[][], int[][], ArrayList[], double[], boolean[], ArrayList) - Method in class edu.cmu.cs.sb.stem.ProfileGui
Responsible for rendering the profile window interface
pmavalues - Variable in class edu.cmu.cs.sb.core.DataSetCore
0 if data value is missing non-zero if present
predictTime(int[], double, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Used to set probability of each state a gene with a TF-binding signature of binding will be in Also computes a record of other statistics based on these predictions
print() - Method in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
Prints the contents of all the variables in the record
print() - Method in class edu.cmu.cs.sb.core.GoAnnotations.GoResults
Prints out the contents of GoResults
printBatchOutputGeneTable(STEM_DataSet) - Method in class edu.cmu.cs.sb.stem.ST
Prints a table for batch output showing for each gene the profile to which it was assigned
printBatchOutputProfileTable(STEM_DataSet) - Method in class edu.cmu.cs.sb.stem.ST
Prints a table for batch output about each profile or k-means cluster
printDefaults(PrintWriter) - Method in class edu.cmu.cs.sb.stem.MAINGUI2
Writes the default settings to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.chromviewer.ChromEnrichmentTable
Writes the content of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Writes the content of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_EdgeTable
Writes the content of the table to a file specified through pw
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Writes the content of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOSplitTable
Writes the content of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOTable
Writes the contents of the table out to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_StaticSummaryTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.DefineGeneSet
Prints those genes currently selected out to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.FilteredTable
Prints the contents of the table in the file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GeneTable
Outputs the content of the PrintWriter
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Writes the contents of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GOTable
Writes the contents of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GOTableExpected
Writes the contents of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.MainTable
Writes the content of the table to a file
printFile(PrintWriter) - Method in class edu.cmu.cs.sb.stem.SortTable
Writes the contents of this table to a file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Writes the gene names to a file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Prints just the gene names to a file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Outputs the list of genes in the table to a file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.stem.FilteredTable
Prints the genes in the table to a file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GeneTable
Print the genes in the table to file
printGeneList(PrintWriter) - Method in class edu.cmu.cs.sb.stem.MainTable
Writes the genes in the table to a file
printGeneNames(PrintWriter) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Writes the names of the genes in the table to a file
printGeneNames(PrintWriter) - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Writes just the gene names to a file
printLevel() - Method in class edu.cmu.cs.sb.core.GoAnnotations
Procedure prints the level of every category in htAncestors
printMinPvals() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Prints the most significant TF-association scores for each TF
printSizes(Component) - Static method in class edu.cmu.cs.sb.core.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
probenames - Variable in class edu.cmu.cs.sb.core.DataSetCore
The list of probe IDs in the current data set
processComponentEvent(ComponentEvent) - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
to process resize of the frame
profileavg - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet
The first index is the profile, the second index is the time point.
ProfileGui - Class in edu.cmu.cs.sb.stem
Class for interface display for all the genes assigned to the same profile
ProfileGui(STEM_DataSet, int, int[], HashSet, int, String, String, String, GenePlotPanel, ChromFrame) - Constructor for class edu.cmu.cs.sb.stem.ProfileGui
Constructor renders the display interface
profilestd - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet
The first index is the profile, the second index is the time point.
profilesumsq - Variable in class edu.cmu.cs.sb.stem.STEM_DataSet
The first index is the profile, the second index is the time point.

R

readColors(BufferedReader) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Loads saved colors for a DREM map
readInitTree(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Initializes the model parameters to those in szinitfileval
readTFGeneData(String) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Responsible for loading the TF-gene interaction input data from the file into the variable fields
redraw() - Method in class edu.cmu.cs.sb.chromviewer.ChromFrame
Redraws the current genes and chromosomes on the interface
reinit(int[][], int[][], int[][], int[][], int[], double[], int) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Reinitialized the variables of the classifier based on the input parameters
removeUnits(String) - Static method in class edu.cmu.cs.sb.core.Util
Removes units after last digit Throws an IllegalArgumentException if no digits in szvalunits
renderDialog(JDialog, String, int, int) - Static method in class edu.cmu.cs.sb.core.Util
Calls renderDialog with Help in the title window for a dialog
renderDialog(JFrame, String, int, int) - Static method in class edu.cmu.cs.sb.core.Util
Calls renderDialog with Help in the title window for a JFrame
renderDialog(JDialog, String, int, int, String) - Static method in class edu.cmu.cs.sb.core.Util
Renders a dialog window with szMessage attached to thedialog at location (noffsetx,noffsety) with title szTtitle
renderDialog(JFrame, String) - Static method in class edu.cmu.cs.sb.core.Util
Calls renderDialog with an offset X value of 25 and an offset Y value of 10
renderDialog(JFrame, String, int, int, String) - Static method in class edu.cmu.cs.sb.core.Util
Renders a dialog window with szMessage attached to theframe at location (noffsetx,noffsety) with title szTtitle
renderDialog(JDialog, String, int, int) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Places szMessage in thedialog window with the title 'Help'
renderDialog(JDialog, String, int, int, String) - Static method in class edu.cmu.cs.sb.drem.DREM_IO
Places szMessage in thedialog window with the title szTitle
renderFilterText() - Method in class edu.cmu.cs.sb.drem.DREMGui
Controls the display of the tex showing the filter information
romanToNumeric(String) - Static method in class edu.cmu.cs.sb.core.Util
function coverts roman numeral strings to integers up to 89.
run() - Method in class edu.cmu.cs.sb.drem.DREM_IO.Downloadfile
Calls getFile with properly formatted URL to download files
run() - Method in class edu.cmu.cs.sb.drem.DREM_IO.Progressdownload
The run method starts the download of the file and updates the download progress
run() - Method in class edu.cmu.cs.sb.stem.ST.Downloadfile
 
run() - Method in class edu.cmu.cs.sb.stem.ST.Progressdownload
 
runBatchDir() - Method in class edu.cmu.cs.sb.stem.ST
Runs STEM on a batch set of default files in szBatchInputDir

S

saveClassifier(String[]) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Returns a string with the classifier parameters
saveColors() - Method in class edu.cmu.cs.sb.drem.DREMGui
Saves the edge color selections to an ouput file
saveString(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Returns a string with the model parameters
searchstage1() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Executes the first phase of the structure search Considers adding and deleting paths, does not consider merges or delays
selectGO(String) - Method in class edu.cmu.cs.sb.drem.DREMGui
Changes the gene visibility based on the selected GO category szSelectedGO
setColumnComparator(Class, Comparator) - Method in class edu.cmu.cs.sb.core.TableSorter
 
setDescription(String) - Method in class edu.cmu.cs.sb.drem.DREMGui_ImageFilter
Sets the value of szdesc
setFilterText() - Method in class edu.cmu.cs.sb.drem.DREMGui
Generates the string in filterText which displays information as to how the genes were selecte
setGeneColors() - Method in class edu.cmu.cs.sb.drem.DREMGui
Sets the colors of the individual genes
setRidge(double) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Sets the value of the ridge parameter
setSigText(TreeSet, PText, int) - Method in class edu.cmu.cs.sb.drem.DREMGui
Sets the text for the significant transcription factors
setSortingStatus(int, int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
setTableHeader(JTableHeader) - Method in class edu.cmu.cs.sb.core.TableSorter
 
setTableModel(TableModel) - Method in class edu.cmu.cs.sb.core.TableSorter
Adds a tableModelListener, clears sorting status, calss fireTableStructureChanged
setValueAt(Object, int, int) - Method in class edu.cmu.cs.sb.core.TableModelSetST
Sets the value in the table in row nrow and column ncol to the contents of value and then calls fireTableCellUpdated.
setValueAt(Object, int, int) - Method in class edu.cmu.cs.sb.core.TableSorter
 
setValueAt(Object, int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel
Sets the value in the table in row nrow and column ncol to the contents of value and then calls fireTableCellUpdated.
setValueAt(Object, int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel
Sets the value in the table in row nrow and column ncol to the contents of value and then calls fireTableCellUpdated.
setValueAt(Object, int, int) - Method in class edu.cmu.cs.sb.drem.DREMGui_PredictModel
Sets the value in the table in row nrow and column ncol to the contents of value and then calls fireTableCellUpdated.
setWidthScale(double) - Method in class edu.cmu.cs.sb.chromviewer.ChromRectangle
Sets the chromosome width
setWidthScale(double) - Method in class edu.cmu.cs.sb.chromviewer.GeneRectangle
Sets the rectangle width
showlabels() - Method in class edu.cmu.cs.sb.drem.DREMGui
Shows all annotation labels
soft(double, double) - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
If abs(da)-ddelta less than or equal to 0 returns 0 otherwise if da is non-negative returns abs(da)-ddelta and otherwide returns -(abs(da)-ddelta)
sortedcorrvals - Variable in class edu.cmu.cs.sb.core.DataSetCore
The distribution of all the average pairwise correlations of genes across full repeats
SortTable - Class in edu.cmu.cs.sb.stem
Class for the interface to select how profiles or cluster of profiles should be sorted
SortTable(JFrame, MAINGUI2, GoAnnotations, STEM_DataSet) - Constructor for class edu.cmu.cs.sb.stem.SortTable
Class constructor - renders the interface
splitdata() - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Splits the non-held out validation data into a training set for learning the model parameters and a test set for model selection
SpringUtilities - Class in edu.cmu.cs.sb.core
Class for manipulating layout Code from http://java.sun.com/docs/books/tutorial/uiswing/examples/layout/SpringGridProject/src/layout/SpringUtilities.java here is the copyright for that code Copyright (c) 1995 - 2008 Sun Microsystems, Inc.
SpringUtilities() - Constructor for class edu.cmu.cs.sb.core.SpringUtilities
 
ST - Class in edu.cmu.cs.sb.stem
Class implementing the main input interface
ST(String, String) - Constructor for class edu.cmu.cs.sb.stem.ST
Constructor for running STEM in batch mode
ST() - Constructor for class edu.cmu.cs.sb.stem.ST
Constructor for running STEM through the normal input interface Renders the interace
ST.Downloadfile - Class in edu.cmu.cs.sb.stem
Inner class controlling the downloading of external files
ST.Progressdownload - Class in edu.cmu.cs.sb.stem
Inner class rendering the progress download display
start - Variable in class edu.cmu.cs.sb.chromviewer.Gene
 
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREM_IO
Responds to a change in the radio button selection specifying the model selection criteria
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet
Responds to changes in the label significance threshold
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_FilterStatic
Responds to changes in the slider specifying the significance threshold
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_GOFilter
Responds to movements in the slider specifying the significance threshold
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions
Responds to state changes on the interface window
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.drem.DREMGui_KeyInputs
Responds to changes in the significance threshold at which transcription factor labels should appears
stateChanged(ChangeEvent) - Method in class edu.cmu.cs.sb.stem.GenePlotPanel
Responds to stateChanged events
StatUtil - Class in edu.cmu.cs.sb.core
The class implements static methods to compute values related to the binomial, hypergeometric, and normal distribution
StatUtil() - Constructor for class edu.cmu.cs.sb.core.StatUtil
 
STEM_DataSet - Class in edu.cmu.cs.sb.stem
Class implementing clustering methods implemented in STEM
STEM_DataSet(DataSetCore, STEM_DataSet) - Constructor for class edu.cmu.cs.sb.stem.STEM_DataSet
Constructor that simply copies all fields in theDataSetCore and theSTEM_DataSet
STEM_DataSet(String, int, double, double, int, int, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class edu.cmu.cs.sb.stem.STEM_DataSet
Constructor for k-means clustering
STEM_DataSet(String, int, double, double, double, double, double, int, int, double, int, long, double[][], int, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class edu.cmu.cs.sb.stem.STEM_DataSet
Constructor for a STEM method clustering
STEM_DataSet.ProfileRec - Class in edu.cmu.cs.sb.stem
Class implements a record for a profile, storing its ID, the number of genes assigned, the number of genes expected, and the uncorrected p-value of the number of genes assigned versus expected
STEM_DataSet.Profilerecdistcomparator - Class in edu.cmu.cs.sb.stem
Compares two profiles records based on their dprofiledist variable
STEM_DataSet.Profilerecdistcomparator() - Constructor for class edu.cmu.cs.sb.stem.STEM_DataSet.Profilerecdistcomparator
 
STEM_GoAnnotations - Class in edu.cmu.cs.sb.stem
Extends GoAnnotations with methods specific to STEM for analyzing GoAnnotations
STEM_GoAnnotations(String, String, String, String, String, String[], String[], int, int, int, String, String, boolean, String, String, boolean, boolean, boolean, boolean) - Constructor for class edu.cmu.cs.sb.stem.STEM_GoAnnotations
Consructor just calls parent constructor
strand - Variable in class edu.cmu.cs.sb.chromviewer.Gene
 
stripLastExtension(String) - Static method in class edu.cmu.cs.sb.core.Util
Returns a string that has the last period and everything after it removed.
szcategoryIDval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The name of the file which maps category IDs to category names that are not official gene ontology categories.
szchromsourceval - Variable in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
 
szchromval - Variable in class edu.cmu.cs.sb.chromviewer.GenomeFileParser
 
szevidenceval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The evidence code input string consisting of evidence codes of annotations to filter, delimited by a comma, pipe, or semicolon
szextraval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The name of the file with additional genes to add to the base set.
szGeneHeader - Variable in class edu.cmu.cs.sb.core.DataSetCore
The header string for the gene name column
szgocategory - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The name of the category
szGoCategoryFile - Variable in class edu.cmu.cs.sb.core.GoAnnotations
This file has the gene Hierarchy
szGoFile - Variable in class edu.cmu.cs.sb.core.GoAnnotations
This file has the gene annotations
szgoid - Variable in class edu.cmu.cs.sb.core.GoAnnotations.GoRec
The ID of the category
szid - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecIDpval
 
szid - Variable in class edu.cmu.cs.sb.core.GoAnnotations.RecIDpval2
 
szID - Variable in class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdrem
 
szInputFile - Variable in class edu.cmu.cs.sb.core.DataSetCore
The designated main data file associated with the set, others are repeats
szName - Variable in class edu.cmu.cs.sb.drem.DREM_GoAnnotations.RecIDdrem
 
szorganismsourceval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Source of the GO annotations
szProbeHeader - Variable in class edu.cmu.cs.sb.core.DataSetCore
The header string for the spot ID column
szSelectedGO - Variable in class edu.cmu.cs.sb.core.GoAnnotations
A string containing the GO ID the profiles are currently sorted by
szsortcommand - Variable in class edu.cmu.cs.sb.core.GoAnnotations
A string containing the current sort command
sztaxonval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The taxon input string consisting of taxons of which to restrict annotations delimited by a comma, pipe, or semicolon
sztermName - Variable in class edu.cmu.cs.sb.core.GoAnnotations.Rec
The name of the category
szxrefsourceval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
Source of the cross-reference
szxrefval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
The name of the file with cross-references equating two or more gene symbols.

T

tableChanged(TableModelEvent) - Method in class edu.cmu.cs.sb.core.TableSorter.TableModelHandler
 
tableModel - Variable in class edu.cmu.cs.sb.core.TableSorter
 
tableModelListener - Variable in class edu.cmu.cs.sb.core.TableSorter
 
TableModelSetST - Class in edu.cmu.cs.sb.core
Class implements a table model, which is used for the define gene set table
TableModelSetST(Object[][], String[], GoAnnotations) - Constructor for class edu.cmu.cs.sb.core.TableModelSetST
Initializes the table model with the data, columnNames, and tga parameters
TableModelSetST(Vector, Vector, GoAnnotations) - Constructor for class edu.cmu.cs.sb.core.TableModelSetST
Initializes the table model with the vector vdata and vcolumnNames parameters converting their contents into arrays.
TableModelST - Class in edu.cmu.cs.sb.core
Class implements a standard table model
TableModelST(Object[][], String[]) - Constructor for class edu.cmu.cs.sb.core.TableModelST
Initializes the table model with the data and columnNames parameters
TableModelST(Vector, Vector) - Constructor for class edu.cmu.cs.sb.core.TableModelST
Initializes the table model with the vector vdata and vcolumnNames parameters converting their contents into arrays.
TableSorter - Class in edu.cmu.cs.sb.core
This class is a modifed version of the Java TableSorter class http://java.sun.com/docs/books/tutorial/uiswing/examples/components/TableSorterDemoProject/src/components/TableSorter.java Copyright for this sample code ============================================================== Copyright (c) 1995 - 2008 Sun Microsystems, Inc.
TableSorter() - Constructor for class edu.cmu.cs.sb.core.TableSorter
Empty class constructor
TableSorter(TableModel) - Constructor for class edu.cmu.cs.sb.core.TableSorter
Class constructor with a table model
TableSorter(TableModel, JTableHeader) - Constructor for class edu.cmu.cs.sb.core.TableSorter
Class constructor with a table model and table header
TableSorter.MouseHandler - Class in edu.cmu.cs.sb.core
 
TableSorter.MouseHandler() - Constructor for class edu.cmu.cs.sb.core.TableSorter.MouseHandler
 
TableSorter.TableModelHandler - Class in edu.cmu.cs.sb.core
 
TableSorter.TableModelHandler() - Constructor for class edu.cmu.cs.sb.core.TableSorter.TableModelHandler
 
TableSorterRoman - Class in edu.cmu.cs.sb.chromviewer
A table sorter for sorting chromosome identifiers
TableSorterRoman() - Constructor for class edu.cmu.cs.sb.chromviewer.TableSorterRoman
Calls empty constructor of parent class
TableSorterRoman(TableModel, int) - Constructor for class edu.cmu.cs.sb.chromviewer.TableSorterRoman
Calls parent class constructor with tableModel; stores nromancol
TableSorterRoman(TableModel, JTableHeader) - Constructor for class edu.cmu.cs.sb.chromviewer.TableSorterRoman
Passes parameters to parent class
tallyassignments() - Method in class edu.cmu.cs.sb.stem.STEM_DataSet
Counts the number of genes assigned to each profile
testhmm(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Evaluates the likelihood of the testdata under the current settings of the model parameters
testhmmHoldOut(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Evaluates the likelihood of the holdoutdata under the current settings of the model parameters
testhmmV(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Evaluates the likelihood of the viterbi assignments of the testdata under the current settings of the model parameters
testhmmVHoldOut(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Evaluates the likelihood of the viterbi assignments of the holdoutdata under the current settings of the model parameters
theChooser - Static variable in class edu.cmu.cs.sb.core.Util
Common chooser object, used across classes so will remember the path
theClusterRecIDpval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
An array of record of GO categories and their best actual enrichment p-values for any cluster of profiles based on last DataSet invoked with
theRecIDdrem - Variable in class edu.cmu.cs.sb.drem.DREM_GoAnnotations
 
theRecIDpval - Variable in class edu.cmu.cs.sb.core.GoAnnotations
An array of record of GO categories and their best actual and expected enrichment p-values for any profile based on last DataSet invoked with
toString() - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Convers the classifier into a string
tpgr - Variable in class edu.cmu.cs.sb.core.GoAnnotations
An array of profiles GO enrichment records ordered based on their enrichment to a GO category
train() - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Calss either trainbin or trainmulti to train the parameters of the classifier
trainbin() - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Trains the parameters in the binary case
trainhmm(DREM_Timeiohmm.Treenode, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Implements a baum-welch method for training the parameters with the current model structure
trainhmmV(DREM_Timeiohmm.Treenode, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Implements a viterbi training method for the parameters with the current model structure
trainmulti() - Method in class edu.cmu.cs.sb.drem.DREM_FastLogistic2
Trains the parameters in the multi-class case
traverse(DREM_Timeiohmm.Treenode, int, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Used for debugging to see the contents of the model
traverseandadd(int[], DREM_Timeiohmm.Treenode, DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
With its helper functions adds the specified path to the model
traverseanddelay(int[], DREM_Timeiohmm.Treenode, int, DREM_Timeiohmm.Treenode, boolean) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
With its helper method traverseanddelayhelp searches for splits to delay one time point Returns true if an eligible split to delay was found
traverseanddelete(int[], DREM_Timeiohmm.Treenode, DREM_Timeiohmm.Treenode, boolean, double, double) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
With its helper function searches for the best path to delete Returns true if an eligible path to delete was found
traverseanddeleteMinPath(int[], int[], DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
With its helper function finds the path with the fewest genes assigned this will become a candidate for deletion
traverseandmerge(int[]) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Responsible with helper functions for merging paths.
TWOPISQRT - Static variable in class edu.cmu.cs.sb.core.StatUtil
Sqrt of 2 times PI

U

unselectGO() - Method in class edu.cmu.cs.sb.drem.DREMGui
Undo gene display based on the GO selection
updateBest(HashMap, HashMap, int, HashMap, double) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Iterates over all the entries in htGoCounts seeing if the current enrichment beats the enrichment in hIDpval and if so updates it
updateBestHyperBinom(HashMap, HashMap, int, HashMap, double, double) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Iterates over all the entries in htGoCounts seeing if the current enrichment beats the enrichment in hIDpval for either the actual size enrichment or expected size enrichment and if so updates it
updateGeneFile(String, String, int[], int, Object) - Method in class edu.cmu.cs.sb.chromviewer.BiomartAccess
Species is the name of the species to download the locations for.
updateParams(DREM_Timeiohmm.Treenode, int, double[][], int[][], int) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Updates the mean, standard deviation, and classifier parameters based on the current expectation of which genes will go through which paths
updateSettings(Vector, boolean) - Method in class edu.cmu.cs.sb.core.ListDialog
Updates the repeat list interface based on the contents of updateData and bupdatealltime
updateSettings() - Method in class edu.cmu.cs.sb.stem.ST
Makes sure all the settings displayed on the interface correspond to the variables internal values.
Util - Class in edu.cmu.cs.sb.core
Class of static utility functions and static variables
Util() - Constructor for class edu.cmu.cs.sb.core.Util
 

V

validEvidence(String, String) - Method in class edu.cmu.cs.sb.core.GoAnnotations
Returns true if szEvidence is not in szevidenceval where the entries of szevidenceval are delimited by a semicolon, comma, or pipe
validVariable(String) - Static method in class edu.cmu.cs.sb.stem.ST
Returns true iff sztype is a valid variable for the defaults file
viterbi(DREM_Timeiohmm.Treenode) - Method in class edu.cmu.cs.sb.drem.DREM_Timeiohmm
Determines the most likely path of each gene through the model

W

writenamesToClipboard() - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Copies the gene names to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Writes just the gene names to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Copies the gene names to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Copies the names of the genes in the table to a clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.stem.FilteredTable
Copies the names in the table to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.stem.GeneTable
Copies the gene name to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Copies just the gene names to the clipboard
writenamesToClipboard() - Method in class edu.cmu.cs.sb.stem.MainTable
Copies the gene names in the file to a clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.chromviewer.ChromEnrichmentTable
Copies the content of the table to a clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable
Copies the contents of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable
Copies the contents of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_EdgeTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GeneTable
Copies the contents of the gene table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GOSplitTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_GOTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_SplitTable
Copies the contents of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.drem.DREMGui_StaticSummaryTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.FilteredTable
Copies the contents of the table to a clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.GeneTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.GOGeneTable
Writes the contents of the table to a clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.GOTable
Copies the contents of the table to a clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.GOTableExpected
Writes the contents of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.MainTable
Copies the content of the table to the clipboard
writeToClipboard() - Method in class edu.cmu.cs.sb.stem.SortTable
Copies the content of this table to the clipboard

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