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[Treebase-guts] SF.net SVN: treebase:[972] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java
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From: <rv...@us...> - 2011-10-13 18:40:34
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Revision: 972
http://treebase.svn.sourceforge.net/treebase/?rev=972&view=rev
Author: rvos
Date: 2011-10-13 18:40:28 +0000 (Thu, 13 Oct 2011)
Log Message:
-----------
Factored out methods to apply default attributes to matrices and characters
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java 2011-10-13 16:26:47 UTC (rev 971)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java 2011-10-13 18:40:28 UTC (rev 972)
@@ -59,15 +59,13 @@
*/
private CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix) {
OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
- CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+ CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+ setMatrixAttributes(xmlMatrix,tbMatrix);
- // attach base uri and history note
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
- xmlMatrix.setBaseURI(mMatrixBaseURI);
-
List<List<DiscreteCharState>> tbStateLabels = tbMatrix.getStateLabels();
List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
for ( int i = 0; i < tbColumns.size(); i++ ) {
+ MatrixColumn tbColumn = tbColumns.get(i);
CharacterStateSet xmlStateSet = xmlMatrix.createCharacterStateSet();
for ( DiscreteCharState tbState : tbStateLabels.get(i) ) {
CharacterState xmlState = xmlStateSet.createCharacterState(tbState.getSymbol().toString());
@@ -77,14 +75,31 @@
attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
}
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
- PhyloChar tbCharacter = tbColumns.get(i).getCharacter();
- if ( null != tbCharacter.getDescription() ) {
- xmlCharacter.setLabel(tbCharacter.getDescription());
- }
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumns.get(i),MatrixColumn.class);
+ setCharacterAttributes(tbColumn, xmlCharacter);
}
return xmlMatrix;
}
+
+ private void setCharacterAttributes(MatrixColumn tbColumn,org.nexml.model.Character xmlCharacter) {
+ PhyloChar tbCharacter = tbColumn.getCharacter();
+ if ( null != tbCharacter.getDescription() ) {
+ xmlCharacter.setLabel(tbCharacter.getLabel());
+ }
+ attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
+ }
+
+ private void setMatrixAttributes(org.nexml.model.Matrix<?> xmlMatrix,CharacterMatrix tbMatrix) {
+ xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
+ xmlMatrix.setBaseURI(mMatrixBaseURI);
+ xmlMatrix.setLabel(tbMatrix.getLabel());
+
+ // attach matrix identifiers
+ attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
+ String tb1MatrixID = tbMatrix.getTB1MatrixID();
+ if ( null != tb1MatrixID ) {
+ ((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix.tb1", Constants.TBTermsURI, tb1MatrixID);
+ }
+ }
/**
* Creates and populates characters (i.e. columns) with their annotations,
@@ -112,11 +127,8 @@
xmlMatrix = getDocument().createMolecularMatrix(xmlOTUs, MolecularMatrix.Protein);
xmlStateSet = ((MolecularMatrix)xmlMatrix).getProteinCharacterStateSet();
}
+ setMatrixAttributes(xmlMatrix,tbMatrix);
- // attach base uri and history note
- xmlMatrix.setBaseURI(mMatrixBaseURI);
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
-
// lookup the equivalent state in tb and attach identifiers
for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
for (DiscreteCharState tbState : tbStateSet.getStates() ) {
@@ -132,7 +144,7 @@
// create columns and attach identifiers
for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
+ setCharacterAttributes(tbColumn, xmlCharacter);
}
return xmlMatrix;
}
@@ -147,19 +159,11 @@
private org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix) {
OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
org.nexml.model.ContinuousMatrix xmlMatrix = getDocument().createContinuousMatrix(xmlOTUs);
+ setMatrixAttributes(xmlMatrix,tbMatrix);
- // attach base uri and history note
- xmlMatrix.setBaseURI(mMatrixBaseURI);
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
-
for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
- PhyloChar tbCharacter = tbColumn.getCharacter();
- if ( null != tbCharacter.getDescription() ) {
- xmlCharacter.setLabel(tbCharacter.getDescription());
- ((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", Constants.DCTermsURI, tbCharacter.getDescription());
- }
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
+ setCharacterAttributes(tbColumn, xmlCharacter);
//coerce the tbMatrix into a character matrix to get its character sets
CharacterMatrix tbCharacterMatrix = (CharacterMatrix)tbMatrix;
@@ -215,12 +219,8 @@
xmlMatrix = fromTreeBaseToXml((ContinuousMatrix) tbMatrix);
populateXmlMatrix((org.nexml.model.ContinuousMatrix)xmlMatrix,(ContinuousMatrix)tbMatrix);
}
- xmlMatrix.setLabel(tbMatrix.getTitle());
- attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
- String tb1MatrixID = tbMatrix.getTB1MatrixID();
- if ( null != tb1MatrixID ) {
- ((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix.tb1", Constants.TBTermsURI, tb1MatrixID);
- }
+
+ // here we copy the character sets for all matrix types
Set<CharSet> tbCharSets = tbMatrix.getCharSets();
for ( CharSet tbCharSet : tbCharSets ) {
Collection<ColumnRange> tbColumnRanges = tbCharSet.getColumns(tbMatrix);
@@ -234,6 +234,12 @@
// increment from beginning to end. This number is probably either null, for a
// contiguous range, or perhaps 3 for codon positions
int tbInc = 1;
+
+ // need to do this to prevent nullpointerexceptions
+ if ( null != tbColumnRange.getRepeatInterval()) {
+ tbInc = tbColumnRange.getRepeatInterval();
+ }
+
// create the equivalent nexml character set
Subset nexSubset = xmlMatrix.createSubset(tbCharSet.getLabel());
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