Package edu.cmu.cs.sb.stem

Class Summary
CompareGui Class for the window that compares profiles
CompareGui.SigComparator Sorts individual profiles by p-value with reference profile in row, then profile ID
CompareGui.SigRowComparator Sorts rows based on reference profile most significant intersection p-value, then profile ID
CompareGui.SupriseRowComparator Sorts rows based on minimum correlation with reference profile, then profile ID
CompareInfo Class encapsulates information on the comparison of two STEM data sets focusing on identifying pairs of profiles with significant intersections between them.
DefineGeneSet Class encapsulates the window slecting which genes to select and unselect
FilteredTable Class for the table of genes that have been filtered
GenePlotPanel Class controls the panel for displaying interface options
GeneTable Class for a table of genes assigned to a profile or cluster
GOGeneTable Class responsible for displaying the genes indicated to be assigned to a GO category in a gene table
GOTable Encapsulates a table for a GO enrichment analysis where enrichment is based on the actual number of genes assigned to a profile.
GOTableExpected Encapsulates a Gene Ontology enrichment analysis where the enrichment calculation is based on the expected number of genes to the profile
MAINGUI2 The class for the overview interface window that shows all the profiles or k-means clusters
MAINGUI2.ProfileComparator The default profile comparison.
MAINGUI2.ProfileexpComparator Compares profiles based on expectected number of genes assigned then by ID
MAINGUI2.ProfileIDComparator Compares profiles based on profile IDs
MAINGUI2.ProfilenumComparator Compares profiles based on number of genes assigned then by ID
MAINGUI2.ProfilesigComparator Compares profiles based on the p-valu signficance, then based on number of genes assigned, number expected, and then ID
MainTable Class which contains table for all genes that were not filtered.
ProfileGui Class for interface display for all the genes assigned to the same profile
SortTable Class for the interface to select how profiles or cluster of profiles should be sorted
ST Class implementing the main input interface
STEM_DataSet Class implementing clustering methods implemented in STEM
STEM_DataSet.ProfileRec 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 Compares two profiles records based on their dprofiledist variable
STEM_GoAnnotations Extends GoAnnotations with methods specific to STEM for analyzing GoAnnotations