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[Treebase-guts] SF.net SVN: treebase:[692] trunk/treebase-core/src/main/java/org/cipres/ treebase
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From: <yo...@us...> - 2010-04-22 18:28:34
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Revision: 692
http://treebase.svn.sourceforge.net/treebase/?rev=692&view=rev
Author: youjun
Date: 2010-04-22 18:28:28 +0000 (Thu, 22 Apr 2010)
Log Message:
-----------
fix: Analysis download scrambles taxon labels - ID: 2970700
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -528,7 +528,7 @@
}
}
pBuilder
- .append(TreebaseUtil.getLineSeparators(2)).append("Study ID = " + pStudy.getId())
+ .append(TreebaseUtil.getLineSeparators(2)).append("TreeBASE Study URI: " + pStudy.getPhyloWSPath().getPurl())
.append("]").append(TreebaseUtil.getLineSeparators(2));
}
}
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 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -600,7 +600,8 @@
public void generateMatrixTable(StringBuilder pBuilder) {
// MATRIX section:
- List<MatrixRow> matrixRows = getRows();
+ List<MatrixRow> matrixRows = new ArrayList<MatrixRow>(getRows());
+ sortRowByTaxonLabel(matrixRows);
Iterator<MatrixRow> iterator = matrixRows.iterator();
ArrayList<String> tLabel = new ArrayList<String>();
@@ -851,7 +852,7 @@
if (isDefaultCodonSet(codonSet)) {
pStrBuilder.append('*');
}
- pStrBuilder.append(" ").append(codonSet.getTitle()).append(" = ").append(TreebaseUtil.LINESEP);
+ pStrBuilder.append(" ").append(codonSet.getTitle()).append(" (CHARACTERS = ").append(StringUtil.tokenize(getTitle())).append(") = ").append(TreebaseUtil.LINESEP);
codonSet.generateNexusString(pStrBuilder);
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -1,6 +1,7 @@
package org.cipres.treebase.domain.matrix;
+import java.util.Comparator;
import java.util.List;
import javax.persistence.AttributeOverride;
@@ -419,7 +420,7 @@
pBuilder.append("BEGIN CHARACTERS;").append(TreebaseUtil.LINESEP);
pBuilder
- .append("[! Matrix ID =").append(getId()).append(" ]").append(TreebaseUtil.LINESEP)
+ .append("[! TreeBASE Matrix URI: ").append(getPhyloWSPath().getPurl()).append("]").append(TreebaseUtil.LINESEP)
.append(TreebaseUtil.LINESEP);
pBuilder.append("\tTITLE ").append(StringUtil.tokenize(getTitle())).append(";").append(
@@ -432,7 +433,7 @@
} else {
taxaTitle = "No taxa found for this matrix. Old data. Need to import this matrix again.";
}
- pBuilder.append("\tLINK TAXA = " + StringUtil.tokenize(taxaTitle) + ";").append(
+ pBuilder.append("\tLINK TAXA = " + StringUtil.tokenize(taxaTitle.replaceAll("Input|Output", "")) + ";").append(
TreebaseUtil.LINESEP);
pBuilder.append(getDimensionsInfo()).append(TreebaseUtil.LINESEP);
@@ -516,4 +517,18 @@
public void setDimensions() {
// By default, do nothing
}
+
+ protected void sortRowByTaxonLabel(List<MatrixRow> rList)
+ {
+ java.util.Collections.sort(rList, new Comparator<MatrixRow>() {
+
+ public int compare(MatrixRow pObject1, MatrixRow pObject2) {
+ String id1 = pObject1.getTaxonLabel().getTaxonLabel();
+ String id2 = pObject2.getTaxonLabel().getTaxonLabel();
+ return id1.compareTo(id2);
+ }
+
+ });
+
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -11,6 +11,8 @@
import javax.persistence.OneToMany;
import javax.persistence.Transient;
+import mesquite.lib.StringUtil;
+
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -74,7 +76,7 @@
@Override
public String getNexusString() {
StringBuilder sb = new StringBuilder();
- sb.append(getNexusPrefix()).append(getTitle()).append(" = ");
+ sb.append(getNexusPrefix()).append(getTitle()).append(" (CHARACTERS = ").append(StringUtil.tokenize(getMatrix().getTitle())).append(") = ");
for (ColumnRange colRange : getColumns()) {
sb.append(" ");
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -2,6 +2,7 @@
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import javax.persistence.AttributeOverride;
@@ -192,11 +193,12 @@
*/
public void buildNexusBlockTaxa(StringBuilder pBuilder, boolean pOnePerLine, boolean pLineNumber) {
- List<TaxonLabel> txnlbllist = getTaxonLabelsReadOnly();
+ List<TaxonLabel> txnlbllist = new ArrayList<TaxonLabel>(getTaxonLabelList());
+ sortByTaxonLabel(txnlbllist);
int numoftxnlbls = txnlbllist.size();
pBuilder.append("BEGIN TAXA;\n");
- pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
+ pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle().replaceAll("Input|Output", "")) + ";\n");
pBuilder.append(" DIMENSIONS NTAX=" + numoftxnlbls + ";\n");
pBuilder.append(" TAXLABELS\n");
pBuilder.append(" ");
@@ -258,4 +260,17 @@
return getTitle();
}
+ private void sortByTaxonLabel(List<TaxonLabel> tList)
+ {
+ java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
+
+ public int compare(TaxonLabel pObject1, TaxonLabel pObject2) {
+ String id1 = pObject1.getTaxonLabel();
+ String id2 = pObject2.getTaxonLabel();
+ return id1.compareTo(id2);
+ }
+
+ });
+
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -557,7 +557,7 @@
pBuilder.append("BEGIN TREES;\n");
pBuilder
.append(" TITLE ").append(StringUtil.tokenize(blockTitle)).append(";\n");
- pBuilder.append(" LINK TAXA = ").append(StringUtil.tokenize(taxaTitle)).append(";\n");
+ pBuilder.append(" LINK TAXA = ").append(StringUtil.tokenize(taxaTitle.replaceAll("Input|Output", ""))).append(";\n");
pBuilder.append(" TREE ").append(StringUtil.tokenize(getLabel())).append(" = ");
if (getRootedTree() != null) {
@@ -569,7 +569,7 @@
}
pBuilder.append(getNewickString()).append("\n");
- pBuilder.append("[! TreeBASE tree Id = ").append(getId()).append(" ]\n");
+ pBuilder.append("[! TreeBASE tree URI: ").append(getPhyloWSPath().getPurl()).append("]\n");
pBuilder.append("\n\nEND;\n");
}
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