[Treebase-guts] SF.net SVN: treebase:[978] trunk

[<hs...@us...>]

Revision: 978
          http://treebase.svn.sourceforge.net/treebase/?rev=978&view=rev
Author:   hshyket
Date:     2011-11-01 16:29:00 +0000 (Tue, 01 Nov 2011)
Log Message:
-----------
Removing translation table from trees Nexus file

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java

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	2011-10-29 13:29:35 UTC (rev 977)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java	2011-11-01 16:29:00 UTC (rev 978)
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 
@@ -260,7 +261,52 @@
 		// }
 
 	}
+	
+	@Transient
+	public void generateAFileDynamicallyNoTranslate(StringBuilder pBuilder) {
 
+		TaxonLabelSet tlSet = getTaxonLabelSet();
+		List<TaxonLabel> txnlbllist = tlSet.getTaxonLabelsReadOnly();
+		int numoftxnlbls = getTaxonNumber();
+
+		String title = getTitle(); 
+		if (TreebaseUtil.isEmpty(title)) {
+			//use the default title:
+			//title = "List of Uploaded Tree Block";
+		}
+		pBuilder.append("BEGIN TREES;\n");
+		pBuilder.append("      TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
+		pBuilder.append("      LINK TAXA = " + StringUtil.tokenize(tlSet.getTitle().replaceAll("Input|Output", "")) + ";\n");
+
+
+		for (PhyloTree atree : getTreeList()) {
+			pBuilder.append("      TREE " + StringUtil.tokenize(atree.getLabel()) + " = ");
+
+			if (atree.getRootedTree() != null) {
+				if (atree.getRootedTree().booleanValue()) {
+					pBuilder.append("[&R] ");
+				} else {
+					pBuilder.append("[&U] ");
+				}
+
+			}
+			String newick = atree.getNewickString();
+			for (int z = 0; z < numoftxnlbls; z++) {
+				newick.concat(StringUtil.tokenize(txnlbllist.get(z).getTaxonLabel()));
+			}
+			// out.append(atree.getNewickString());
+			pBuilder.append(newick);
+			pBuilder.append("\n");
+		}
+		pBuilder.append("\n\n\nEND;\n");
+
+		// File did not exist and was created
+		// } else {
+		// File already exists
+		// }
+
+	}
+
 	@Transient
 	public String getTaxonLabelSetTitle() {
 		return getTaxonLabelSet().getTitle();

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2011-10-29 13:29:35 UTC (rev 977)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2011-11-01 16:29:00 UTC (rev 978)
@@ -190,11 +190,14 @@
 				Set<PhyloTree> trees =  treeResults.getResults();
 				TreeBlock treeBlock = new TreeBlock();
 				TaxonLabelSet taxonLabelSet = new TaxonLabelSet();
+				List<String> taxonLabels = new ArrayList<String>();
+
 				
 				for (PhyloTree pTree : trees) {
 					for (TaxonLabel pTaxLabel : pTree.getTreeBlock().getTaxonLabelList()) {
-						if (! taxonLabelSet.getTaxonLabelsReadOnly().contains(pTaxLabel)) {
-							taxonLabelSet.addPhyloTaxonLabel(pTaxLabel);	
+						if (! taxonLabels.contains(pTaxLabel.getTaxonLabel())) {
+							taxonLabelSet.addPhyloTaxonLabel(pTaxLabel);
+							taxonLabels.add(pTaxLabel.getTaxonLabel());				
 						}
 					}
 					treeBlock.addPhyloTree(pTree);	
@@ -208,7 +211,7 @@
 			
 				taxonLabelSet.buildNexusBlockTaxa(builder, true, false);
 			
-				treeBlock.generateAFileDynamically(builder);
+				treeBlock.generateAFileDynamicallyNoTranslate(builder);
 				fileName += ".nex";
 			}
 			

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