Annotation Parser Dependencies
From Informatics
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Usage analysis of Class
org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
Data Structure Dependencies
Values used during file loading
The Locus Link and Abbreviation values are used by the CSExprMicroarraySet:
org.geworkbench.bison.datastructure.biocollections.microarrays (6 usages) CSExprMicroarraySet.CMicroarrayParser (5 usages) executeLine(String, DSMicroarraySet<DSMicroarray>) (4 usages) (285, 43) String[] result = AnnotationParser.getInfo(token, AnnotationParser.LOCUSLINK); (285, 75) String[] result = AnnotationParser.getInfo(token, AnnotationParser.LOCUSLINK); (298, 46) String[] geneNames = AnnotationParser.getInfo(token, AnnotationParser.ABREV); (298, 78) String[] geneNames = AnnotationParser.getInfo(token, AnnotationParser.ABREV);
Locus Link is set as the Unigene value:
markerVector.get(currGeneId).getUnigene().set(token);
If the locus is not empty, it is also set as the gene id:
markerVector.get(currGeneId).setGeneId(Integer.parseInt(locus));
The Abbreviation field is set as the gene's name:
markerVector.get(currGeneId).setGeneName(geneNames[0]);
Values used outside of file loading
Unfortunately, on top of attempting to use the Locus Link values during initial file parsing, each call of getGeneId(), getCanonicalLabel(), and getShortName() results in another parsing of the loaded annotations. This happens in the following spots:
org.geworkbench.bison.datastructure.bioobjects.markers (5 usages) CSExpressionMarker (2 usages) getGeneId() (2 usages) (176, 31) String uni = (AnnotationParser.getInfo(label, AnnotationParser.LOCUSLINK)[0]); (176, 63) String uni = (AnnotationParser.getInfo(label, AnnotationParser.LOCUSLINK)[0]); CSGeneMarker (3 usages) getCanonicalLabel() (2 usages) (301, 28) String text1 = AnnotationParser.getInfo(label, AnnotationParser.DESCRIPTION)[0]; (301, 60) String text1 = AnnotationParser.getInfo(label, AnnotationParser.DESCRIPTION)[0]; getShortName() (1 usage) (174, 23) String name = AnnotationParser.getGeneName(label);
Also, when setting the the value of a CSUnigene object, annotations are parsed again and your input may be ignored:
public void set(DSGeneMarker marker) {
if (unigeneId == -1) {
try {
String[] annots = AnnotationParser.getInfo(marker.getLabel(), AnnotationParser.UNIGENE);
String uni = "";
if ((annots != null) && (annots.length > 0)) {
uni = annots[0];
if (uni.compareTo("") != 0) {
String[] unigeneStrings = uni.split("\\.");
if (unigeneStrings.length > 1) {
organism = organisms.indexOf(unigeneStrings[0]);
unigeneId = Integer.parseInt(unigeneStrings[1]);
} else {
unigeneId = -marker.getSerial();
}
} else {
this.unigeneId = -marker.getSerial();
}
} else {
this.unigeneId = -marker.getSerial();
}
} catch (Exception e) {
System.out.println("error parsing " + marker.getLabel());
e.printStackTrace();
unigeneId = -marker.getSerial();
}
}
}
GO Terms
The GO terms tree is built during annotation file parsing and serialized:
org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser (1 usage) AnnotationParser (1 usage) createNewGoTable() (1 usage) (615, 41) String[] info = getInfo(id, AnnotationParser.GOTERM);
Also, the GO Terms components makes several references to the Annotations parser during it's operation, although most of these are references that do not cause further parsing, just refer to already parsed data:
org.geworkbench.components.goterms (16 usages)
GOPanel (16 usages)
addGotermPanel(GoTerm, boolean, boolean) (1 usage)
(1211, 37) String id = AnnotationParser.geneNameMap.get(marker.
buildAndMapTree() (1 usage)
(1108, 33) count = AnnotationParser.affyIDs.size();
computePValueTrends() (1 usage)
(1894, 71) if (go.getSelected() > 0 && selectedList.contains(AnnotationParser.getGeneName(affyid).trim())) {
geneList_mouseClicked(MouseEvent) (1 usage)
(1282, 29) String id = AnnotationParser.geneNameMap.get(marker.getLabel()).get(0);
getSelectedUniqueGenesCount() (3 usages)
(2014, 39) String geneName = AnnotationParser.getGeneName(affyid.trim());
(2019, 39) Set<String> affyids = AnnotationParser.affyIDs.keySet();
(2021, 39) String geneName = AnnotationParser.getGeneName(affyid.trim());
getTotalUniqueGenesCount() (3 usages)
(1993, 35) String geneName = AnnotationParser.getGeneName(affyid.trim());
(1999, 35) Set<String> affyids = AnnotationParser.affyIDs.keySet();
(2001, 35) String geneName = AnnotationParser.getGeneName(affyid.trim());
jChipTypeComboBox_actionPerformed(ActionEvent) (3 usages)
(1732, 13) if (AnnotationParser.getChipType() != null && !AnnotationParser.getChipType().equals(chipType))
(1732, 56) if (AnnotationParser.getChipType() != null && !AnnotationParser.getChipType().equals(chipType))
(1733, 13) AnnotationParser.setChipType(chiptype);
mapNode(DefaultMutableTreeNode, Vector) (1 usage)
(2039, 51) Vector<String> aids = (Vector<String>)AnnotationParser.getGotable().get(go.getId());
mapReferenceList() (1 usage)
(1404, 28) HashMap affyhash = AnnotationParser.getGotable();
mapTree() (1 usage)
(1452, 26) HashMap affyhash=AnnotationParser.getGotable();
org.geworkbench.components.goterms.annotation (2 usages)
GoTerm (2 usages)
addGeneName(String) (1 usage)
(233, 31) String geneName = AnnotationParser.getGeneName(affyid.trim());
addSelected(String) (1 usage)
(106, 27) String geneName = AnnotationParser.getGeneName(id.trim());
Components
GO Panel
For some reason the GO panel does it's own parsing and handling of the chiptype map file:
org.geworkbench.components.goterms (1 usage)
GOPanel (1 usage)
jbInit() (1 usage)
(454, 21) AnnotationParser.class.getResourceAsStream("chiptypeMap.txt")));
Pathway Decoder and Reverse Engineering
Gene networks will display information from the annotations instead of from the data file if it has been loaded:
org.geworkbench.components.pathwaydecoder (16 usages)
GeneNetwork (6 usages)
this_mouseReleased(MouseEvent) (6 usages)
(201, 47) String[] sn = AnnotationParser.getInfo(affyId, AnnotationParser.DESCRIPTION);
(201, 80) String[] sn = AnnotationParser.getInfo(affyId, AnnotationParser.DESCRIPTION);
(217, 54) String[] processes = AnnotationParser.getInfo(affyId, AnnotationParser.PATHWAY);
(217, 87) String[] processes = AnnotationParser.getInfo(affyId, AnnotationParser.PATHWAY);
(235, 54) String[] functions = AnnotationParser.getInfo(affyId, AnnotationParser.GOTERM);
(235, 87) String[] functions = AnnotationParser.getInfo(affyId, AnnotationParser.GOTERM);
GenePairPlot (4 usages)
drawChart(int, int) (4 usages)
(322, 22) label1 = AnnotationParser.getInfo(getMicroarraySet().getMarkers().get(id1).getLabel(), AnnotationParser.DESCRIPTION)[0];
(322, 100) label1 = AnnotationParser.getInfo(getMicroarraySet().getMarkers().get(id1).getLabel(), AnnotationParser.DESCRIPTION)[0];
(323, 22) label2 = AnnotationParser.getInfo(getMicroarraySet().getMarkers().get(id2).getLabel(), AnnotationParser.DESCRIPTION)[0];
(323, 100) label2 = AnnotationParser.getInfo(getMicroarraySet().getMarkers().get(id2).getLabel(), AnnotationParser.DESCRIPTION)[0];
GeneProfiler (4 usages)
getChart(GeneNetworkEdgeImpl, int, int) (4 usages)
(923, 22) label1 = AnnotationParser.getInfo(maSet.get(rc.getId1()).getLabel(), AnnotationParser.DESCRIPTION)[0];
(923, 82) label1 = AnnotationParser.getInfo(maSet.get(rc.getId1()).getLabel(), AnnotationParser.DESCRIPTION)[0];
(924, 22) label2 = AnnotationParser.getInfo(rc.getMarker2().getLabel(), AnnotationParser.DESCRIPTION)[0];
(924, 75) label2 = AnnotationParser.getInfo(rc.getMarker2().getLabel(), AnnotationParser.DESCRIPTION)[0];
HighLowAnalysisPanel (2 usages)
setListHeaders() (2 usages)
(691, 30) markerName = AnnotationParser.getInfo(marker.getLabel(), AnnotationParser.DESCRIPTION);
(691, 74) markerName = AnnotationParser.getInfo(marker.getLabel(), AnnotationParser.DESCRIPTION);
Sequence Retriever
The sequence retriever uses the annotations to get the Swiss Prot ID:
org.geworkbench.components.sequenceretriever (2 usages)
SequenceRetriever (2 usages)
getAffyProteinSequences(String, BufferedWriter) (2 usages)
(411, 35) String[] uniprotids = AnnotationParser.getInfo( affyid, AnnotationParser.SWISSPROT );
(411, 69) String[] uniprotids = AnnotationParser.getInfo( affyid, AnnotationParser.SWISSPROT );
