treebase-guts

[Treebase-guts] SF.net SVN: treebase:[568] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/matrix/CharacterMatrix.java

[<rv...@us...>]

Revision: 568
          http://treebase.svn.sourceforge.net/treebase/?rev=568&view=rev
Author:   rvos
Date:     2010-03-15 01:00:44 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Added getAnnotations() and getLabel() for nexml and rdf serialization.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java	2010-03-12 23:44:43 UTC (rev 567)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java	2010-03-15 01:00:44 UTC (rev 568)
@@ -31,7 +31,9 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.Annotation;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
 
 /**
@@ -931,4 +933,20 @@
 	@Override
 	@Transient
 	public boolean isCharacterMatrix() { return true; }
+	
+	@Transient
+	public List<Annotation> getAnnotations() {
+		List<Annotation> annotations = super.getAnnotations();
+		annotations.add(new Annotation(Constants.TBTermsURI,"tb:type.matrix",getDataType().getDescription()));
+		annotations.add(new Annotation(Constants.TBTermsURI,"tb:ntax.matrix",getnTax()));
+		annotations.add(new Annotation(Constants.TBTermsURI,"tb:nchar.matrix",getnChar()));
+		annotations.add(new Annotation(Constants.TBTermsURI,"tb:identifier.matrix",getId()));
+		return annotations;
+	}	
+	
+	@Transient
+	public String getLabel() {
+		return getTitle();
+	}
+	
 }


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[Treebase-guts] SF.net SVN: treebase:[902] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/matrix/CharacterMatrix.java

[<rv...@us...>]

Revision: 902
          http://treebase.svn.sourceforge.net/treebase/?rev=902&view=rev
Author:   rvos
Date:     2011-06-08 14:01:38 +0000 (Wed, 08 Jun 2011)

Log Message:
-----------
The Set that contains all CharSets associated with the matrix should be parameterized to Set<CharSet> to avoid warnings about this. I also commented out a private method that is never used locally (and therefore useless).

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java	2011-06-08 13:59:18 UTC (rev 901)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java	2011-06-08 14:01:38 UTC (rev 902)
@@ -48,6 +48,11 @@
 @DiscriminatorValue("C")
 public abstract class CharacterMatrix extends Matrix {
 
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+
 	protected List<MatrixRow> mRows = new ArrayList<MatrixRow>();
 
 	private AncStateSet mDefaultAncSet;
@@ -58,7 +63,7 @@
 
 	private List<MatrixColumn> mColumns = new ArrayList<MatrixColumn>();
 	private Set<AncStateSet> mAncStateSets = new HashSet<AncStateSet>();
-	private Set mCharSets = new HashSet();
+	private Set<CharSet> mCharSets = new HashSet<CharSet>();
 	private Collection<CharWeightSet> mWeightSets = new ArrayList<CharWeightSet>();
 	private Collection<CodonPositionSet> mCodonPosSets = new ArrayList<CodonPositionSet>();
 	private Collection<GeneticCodeSet> mCodeSets = new ArrayList<GeneticCodeSet>();
@@ -158,9 +163,10 @@
 	 * @param pExSet
 	 * @return
 	 */
-	private boolean isDefaultExcludedSet(ExcludedCharSet pExSet) {
-		return (pExSet == getDefaultExcludedSet());
-	}
+// this is never used locally, so I commented it out - maybe it shouldn't be here? -- rav, 8 June '11
+//	private boolean isDefaultExcludedSet(ExcludedCharSet pExSet) {
+//		return (pExSet == getDefaultExcludedSet());
+//	}
 	
 	/**
 	 * Return the DefaultTypeSet field.
@@ -258,14 +264,14 @@
 	@OneToMany(mappedBy = "matrix", cascade = {CascadeType.MERGE, CascadeType.PERSIST,
 		CascadeType.REMOVE}, targetEntity = CharSet.class)
 	@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "matrixCache")
-	public Set getCharSets() {
+	public Set<CharSet> getCharSets() {
 		return mCharSets;
 	}
 
 	/**
 	 * Set the CharSets field.
 	 */
-	public void setCharSets(Set pNewCharSets) {
+	public void setCharSets(Set<CharSet> pNewCharSets) {
 		mCharSets = pNewCharSets;
 	}
 


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