@groovy.util.logging.Log class GapAnnotator extends RegulatingActor<CoverageBlock>
Annotates regions with gene, transcript, CDS overlap and distance information, as well as custom annotation to gene associations ("panels") and sub-panels (groups of genes within a panel)
| Type | Name and description |
|---|---|
static java.util.List<java.lang.String> |
ANNOTATION_COLUMNSNames of properties set as annotations on gap regions |
static java.util.List<java.lang.String> |
ANNOTATION_OUTPUT_COLUMNSPrettier human readable version of above columns - should always match 1-1 |
java.util.ArrayList<java.lang.String> |
panelClassesList of all known sub panels ("panel classes") |
java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.util.List>> |
panelGeneMapMap keyed on gene to a nested lookup table that is keyed on panel name and returns the list of subpanels from the major panel that include the gene. |
RefGenes |
refgenes |
| Constructor and description |
|---|
GapAnnotator
(RefGenes refgenes) |
GapAnnotator
(RefGenes refgenes, java.util.ArrayList<java.lang.String> panelFiles) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
java.util.List<java.util.Map> |
annotateGapRegion(gngs.Region blockRegion) |
|
Regions |
getExonsForTranscript(java.lang.String tx) |
|
java.util.Map<java.lang.String, java.lang.Object> |
getPanelAnnotations(java.lang.String gene) |
|
void |
indexPanels(java.util.List<java.lang.String> panelFiles) |
|
void |
indexPanels(java.util.List<java.lang.String> panelClassNames, java.util.List<java.util.List<java.util.Map>> tsvs) |
|
void |
process(CoverageBlock block) |
Names of properties set as annotations on gap regions
Prettier human readable version of above columns - should always match 1-1
List of all known sub panels ("panel classes")
Map keyed on gene to a nested lookup table that is keyed on panel name and returns the list of subpanels from the major panel that include the gene.
Groovy Documentation