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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 |