edu.cmu.cs.sb.stem
Class STEM_GoAnnotations

java.lang.Object
  extended by edu.cmu.cs.sb.core.GoAnnotations
      extended by edu.cmu.cs.sb.stem.STEM_GoAnnotations

public class STEM_GoAnnotations
extends GoAnnotations

Extends GoAnnotations with methods specific to STEM for analyzing GoAnnotations


Nested Class Summary
 
Nested classes/interfaces inherited from class edu.cmu.cs.sb.core.GoAnnotations
GoAnnotations.GORankingComparator, GoAnnotations.GoRec, GoAnnotations.GoResults, GoAnnotations.ProfileGORankingRec, GoAnnotations.Rec, GoAnnotations.RecCompare, GoAnnotations.RecCompareBinom, GoAnnotations.RecCount, GoAnnotations.RecIDpval, GoAnnotations.RecIDpval2
 
Field Summary
 
Fields inherited from class edu.cmu.cs.sb.core.GoAnnotations
algoAll, algoAllbase, bactual, bcluster, bcontoval, bfontoval, bpontoval, brandomgoval, extragenes, extraprobes, goAll, htAlt, htAncestors, htFullCount, htGeneNames, htGO, htGoLabels, htIDCategory, nGeneSet, nlegalgo, nmaxsize, nmingo, nmingolevel, nsamplespval, numcategory, numtotalgenes, szcategoryIDval, szevidenceval, szextraval, szGoCategoryFile, szGoFile, szorganismsourceval, szSelectedGO, szsortcommand, sztaxonval, szxrefsourceval, szxrefval, theClusterRecIDpval, theRecIDpval, tpgr
 
Constructor Summary
STEM_GoAnnotations(java.lang.String szorganismsourceval, java.lang.String szxrefsourceval, java.lang.String szxrefval, java.lang.String szGoFile, java.lang.String szGoCategoryFile, java.lang.String[] baseGenes1, java.lang.String[] baseProbes1, int nsamplespval, int nmingo, int nmingolevel, java.lang.String szextraval, java.lang.String szcategoryIDval, boolean bspotincluded, java.lang.String szevidenceval, java.lang.String sztaxonval, boolean bpontoval, boolean bcontoval, boolean bfontoval, boolean brandomgoval)
          Consructor just calls parent constructor
 
Method Summary
 void computeBestPvaluesClustersProfiles(STEM_DataSet theDataSet)
          Loads theRecIDpval and theClusterRecIDpval to have the p-values for the most enriched profiles and clusters for each category
 GoAnnotations.GoResults getCategory(java.util.ArrayList profileList, java.util.ArrayList[] ids, java.lang.String[] genenames, java.util.ArrayList[] assignments, boolean bqueryset, java.util.HashSet htinames)
          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
 void getProfileRankings(java.util.ArrayList clustersofprofilesnum, java.util.ArrayList[] profilesAssigned, java.lang.String[] genenames, java.util.ArrayList[] assignments, double[] expectedassignments)
          Puts in tpgr a sorted ranking of profiles based on the current sort by seelctions
 
Methods inherited from class edu.cmu.cs.sb.core.GoAnnotations
addgenesgo, addgenesgocategory, addOfficialLine, addprobegenemap, buildxref, computePValues, computePValues, computePValuesBase, containsTaxon, geneIsOfType, getCategory, getCategory, getCategory, getCategory, getgocategories, getLevel, hashtoList1, hashtoList2, incrementSelectData, isOrder, labelsForID, levelGO, loadID, loadIDbase, loadIDCategory, printLevel, updateBest, updateBestHyperBinom, validEvidence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

STEM_GoAnnotations

public STEM_GoAnnotations(java.lang.String szorganismsourceval,
                          java.lang.String szxrefsourceval,
                          java.lang.String szxrefval,
                          java.lang.String szGoFile,
                          java.lang.String szGoCategoryFile,
                          java.lang.String[] baseGenes1,
                          java.lang.String[] baseProbes1,
                          int nsamplespval,
                          int nmingo,
                          int nmingolevel,
                          java.lang.String szextraval,
                          java.lang.String szcategoryIDval,
                          boolean bspotincluded,
                          java.lang.String szevidenceval,
                          java.lang.String sztaxonval,
                          boolean bpontoval,
                          boolean bcontoval,
                          boolean bfontoval,
                          boolean brandomgoval)
                   throws java.io.FileNotFoundException,
                          java.io.IOException,
                          java.lang.IllegalArgumentException
Consructor just calls parent constructor

Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.IllegalArgumentException
Method Detail

getCategory

public GoAnnotations.GoResults getCategory(java.util.ArrayList profileList,
                                           java.util.ArrayList[] ids,
                                           java.lang.String[] genenames,
                                           java.util.ArrayList[] assignments,
                                           boolean bqueryset,
                                           java.util.HashSet htinames)
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


getProfileRankings

public void getProfileRankings(java.util.ArrayList clustersofprofilesnum,
                               java.util.ArrayList[] profilesAssigned,
                               java.lang.String[] genenames,
                               java.util.ArrayList[] assignments,
                               double[] expectedassignments)
Puts in tpgr a sorted ranking of profiles based on the current sort by seelctions


computeBestPvaluesClustersProfiles

public void computeBestPvaluesClustersProfiles(STEM_DataSet theDataSet)
Loads theRecIDpval and theClusterRecIDpval to have the p-values for the most enriched profiles and clusters for each category