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[Treebase-guts] SF.net SVN: treebase:[1014] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain
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From: <rv...@us...> - 2012-01-19 22:38:23
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Revision: 1014
http://treebase.svn.sourceforge.net/treebase/?rev=1014&view=rev
Author: rvos
Date: 2012-01-19 22:38:16 +0000 (Thu, 19 Jan 2012)
Log Message:
-----------
Adding interface method and implementations for getStudy(). This so we can determine for any object i. whether it logically belongs to a Study (e.g. User objects don't, but trees do) ii. subsequently whether the data object is under embargo.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TBPersistable.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStep.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedData.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -18,6 +18,7 @@
import org.cipres.treebase.PhyloWSPath;
import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.study.Study;
import org.hibernate.annotations.GenericGenerator;
/**
@@ -165,4 +166,12 @@
return this.getNamespacedGUID().toString();
}
+ /*
+ * (non-Javadoc)
+ * @see org.cipres.treebase.domain.TBPersistable#getStudy()
+ */
+ public Study getStudy() {
+ return null;
+ }
+
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TBPersistable.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TBPersistable.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TBPersistable.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -4,6 +4,7 @@
import org.cipres.treebase.NamespacedGUID;
import org.cipres.treebase.PhyloWSPath;
import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.domain.study.Study;
/**
* A tagging interface for all persisted treebase objects.
@@ -31,11 +32,6 @@
public static final int CITATION_TITLE_COLUMN_LENGTH = 500;
public static final int CITATION_ABSTRACT_COLUMN_LENGTH = 10000;
- /**
- * Return the id.
- *
- * @return
- */
public Long getId();
public TreebaseIDString getTreebaseIDString ();
@@ -44,6 +40,20 @@
public PhyloWSPath getPhyloWSPath ();
+ /**
+ * Is an object that implements this is logically
+ * part of a containing object (e.g. a node is part
+ * of a tree), this method returns that containing
+ * object.
+ * @return
+ */
public TBPersistable getContext ();
+
+ /**
+ * If an object that implements this logically belongs to a Study,
+ * this method returns that Study. Otherwise returns null.
+ * @return
+ */
+ public Study getStudy();
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/DistanceMatrixElement.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -12,6 +12,7 @@
import org.hibernate.annotations.CacheConcurrencyStrategy;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
/**
@@ -113,5 +114,9 @@
public void setMatrix(DistanceMatrix pNewMatrix) {
mMatrix = pNewMatrix;
}
+
+ public Study getStudy() {
+ return getMatrix().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -23,6 +23,7 @@
import org.hibernate.annotations.Index;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.study.Study;
/**
* MatrixColumn.java
@@ -153,4 +154,9 @@
if (theMatrix == null) { return null; }
return theMatrix.getColumnsReadOnly().indexOf(this);
}
+
+ @Transient
+ public Study getStudy() {
+ return getMatrix().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -25,6 +25,7 @@
import org.hibernate.annotations.Index;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.study.Study;
/**
* MatrixElement.java
@@ -157,4 +158,9 @@
public CharacterMatrix getContext() {
return getColumn().getMatrix();
}
+
+ @Transient
+ public Study getStudy() {
+ return getContext().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -5,6 +5,7 @@
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import javax.persistence.AttributeOverride;
@@ -28,6 +29,7 @@
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
/**
@@ -149,10 +151,14 @@
/**
* Represents all the elements as symbols in one string.
- * For one character one symbol, This can handle 512k size of characters in a matrix.
+ * This can handle 512k size of characters in a matrix.
*
* It is precalculated and stored for faster generating nexus blocks.
*
+ * Note that for ambiguous states (e.g. N in a DNA sequence) this
+ * returns a list of all fundamental states that comprise the ambiguous
+ * state, i.e. instead of N, this returns {ACGT}
+ *
* @return String
*/
@Lob
@@ -160,6 +166,51 @@
public String getSymbolString() {
return mSymbolString;
}
+
+
+ /**
+ * Represents all the elements as symbols in one string.
+ *
+ * Note that this method post-processes the output of getSymbolString(), i.e.
+ * if that method returns an {ACGT} this method replaces that with whatever
+ * ambiguity mapping was provided. E.g. if the map pMapping holds a slot for
+ * "ACGT" => "N" this method will return that N instead.
+ *
+ * @return String
+ */
+ @Transient
+ public String getSymbolString(Map<String,String> pMapping) {
+ String inputString = getSymbolString();
+ StringBuffer outputString = new StringBuffer();
+ List<Character> ambiguous = new ArrayList<Character>();
+ boolean isAmbiguous = false;
+ for ( int i = 0; i < inputString.length(); i++ ) {
+ char current = inputString.charAt(i);
+ if ( current == '{' ) {
+ isAmbiguous = true;
+ ambiguous.clear();
+ continue;
+ }
+ if ( current == '}' ) {
+ isAmbiguous = false;
+ Collections.sort(ambiguous);
+ StringBuffer ambigBuffer = new StringBuffer();
+ ambigBuffer.append(ambiguous.toArray(new Character[ambiguous.size()]));
+ String ambigString = ambigBuffer.toString();
+ if ( pMapping.containsKey(ambigString) ) {
+ outputString.append(pMapping.get(ambigString));
+ }
+ continue;
+ }
+ if ( isAmbiguous ) {
+ ambiguous.add(current);
+ }
+ else {
+ outputString.append(current);
+ }
+ }
+ return outputString.toString();
+ }
/**
* Set the SymbolString field.
@@ -356,4 +407,9 @@
if (syms == null) { return "(no data)"; }
return syms.length() >= DISPLAY_STRING_LENGTH ? syms.substring(0, DISPLAY_STRING_LENGTH) : syms;
}
+
+ @Transient
+ public Study getStudy() {
+ return getMatrix().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -23,6 +23,7 @@
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.TBPersistable;
import org.cipres.treebase.domain.matrix.RowSegmentService.RowSegmentField;
+import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.SpecimenLabel;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.framework.ExecutionResult;
@@ -563,4 +564,9 @@
public void setChecked(boolean pChecked) {
mChecked = pChecked;
}
+
+ @Transient
+ public Study getStudy() {
+ return getMatrixRow().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStep.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStep.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalysisStep.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -354,5 +354,10 @@
if (index == -1) return null;
return index;
}
+
+ @Transient
+ public Study getStudy() {
+ return getAnalysis().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedData.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedData.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/AnalyzedData.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -161,4 +161,9 @@
*/
@Transient
public abstract String getDisplayName();
+
+ @Transient
+ public Study getStudy() {
+ return getAnalysisStep().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -748,5 +748,10 @@
}
return annotations;
}
+
+ @Transient
+ public Study getStudy() {
+ return this;
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -24,6 +24,7 @@
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
/**
@@ -606,4 +607,9 @@
return getTree();
}
*/
+
+ @Transient
+ public Study getStudy() {
+ return getTree().getStudy();
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2012-01-11 17:02:42 UTC (rev 1013)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2012-01-19 22:38:16 UTC (rev 1014)
@@ -346,5 +346,10 @@
}
return null;
}
+
+ @Transient
+ public Study getStudy() {
+ return getContext();
+ }
}
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