[Treebase-guts] SF.net SVN: treebase:[1003] trunk/treebase-core/src

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

Revision: 1003
          http://treebase.svn.sourceforge.net/treebase/?rev=1003&view=rev
Author:   hshyket
Date:     2011-12-12 18:01:09 +0000 (Mon, 12 Dec 2011)
Log Message:
-----------
Fixing issue where the numbering of the translation table in the tree string was not converting properly

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
    trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java

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	2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java	2011-12-12 18:01:09 UTC (rev 1003)
@@ -260,7 +260,7 @@
 		return getTitle();
 	}
 
-	private void sortByTaxonLabel(List<TaxonLabel> tList)
+	public void sortByTaxonLabel(List<TaxonLabel> tList)
 	{
 		java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
 			
@@ -273,4 +273,16 @@
 		});
 		
 	}
+	
+	public void sortByTaxonLabelLength(List<TaxonLabel> tList)
+	{
+		java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
+			
+			public int compare(TaxonLabel pObject1, TaxonLabel pObject2) {
+				return pObject2.getTaxonLabel().length() - pObject1.getTaxonLabel().length();
+			}
+		
+		});
+		
+	}
 }

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	2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java	2011-12-12 18:01:09 UTC (rev 1003)
@@ -244,11 +244,18 @@
 
 			}
 			String tmpnewick, newick = atree.getNewickString();
+			List<TaxonLabel> txnlbllistclone = new ArrayList<TaxonLabel>(txnlbllist);
+			tlSet.sortByTaxonLabelLength(txnlbllistclone);
+			HashMap<String, Integer> txnOrder = new HashMap<String, Integer>();
+			for (int y = 0; y < numoftxnlbls; y++) {
+				txnOrder.put(txnlbllist.get(y).getTaxonLabel(), y);
+			}
 			for (int z = 0; z < numoftxnlbls; z++) {
-				String label = StringUtil.tokenize(txnlbllist.get(z).getTaxonLabel());
-				tmpnewick = newick.replace(label, String.valueOf(z + 1));
+				String label = StringUtil.tokenize(txnlbllistclone.get(z).getTaxonLabel());
+				tmpnewick = newick.replace(label, String.valueOf(txnOrder.get(txnlbllistclone.get(z).getTaxonLabel())+1));
 				newick = tmpnewick;
 			}
+			txnlbllistclone = null;
 			// out.append(atree.getNewickString());
 			pBuilder.append(newick);
 			pBuilder.append("\n");

Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java	2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java	2011-12-12 18:01:09 UTC (rev 1003)
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import org.apache.log4j.Logger;
 import org.cipres.treebase.dao.AbstractDAOTest;
@@ -112,17 +113,49 @@
 		}
 		assertTrue(matricesOkay);
 	}
+		
+	public void testTaxonLabelLengthSorting() {
+		int x = 0;
+		boolean isTaxonSorted = false;
+		
+		List<TaxonLabel> res = (List<TaxonLabel>) findHomoSapiensTL();
+		LOGGER.info("Homo matrices: " + res.size() + " result(s)");
+		assertNotNull(res);
+		TaxonLabel newTaxon = new TaxonLabel();
+		newTaxon.setTaxonLabel("Homo Sapiens ABCD");
+		res.add(newTaxon);
+		//res.get(1).setTaxonLabel("Homo Sapiens ABCD");
+		TaxonLabelSet tlSet = new TaxonLabelSet();
+		tlSet.sortByTaxonLabelLength(res);
+		
+		//for (TaxonLabel tLabel : res) {
+		for (x = 0; x < res.size(); x++) {
+			if (x > 0) {
+				if (res.get(x-1).getTaxonLabel().length() >= res.get(x).getTaxonLabel().length()) {		
+					isTaxonSorted = true;
+				}
+				else {
+					LOGGER.debug("Taxon Labels are not sorted");
+					isTaxonSorted = false;
+					break;
+				}
+			}
+		}	
+		assertTrue(isTaxonSorted);
+	}
 	
 	
 	private Collection<TaxonLabel> findHomoSapiensTL() {
 		return getTaxonLabelHome().findByExactString("Homo sapiens");
 	}
-	
+		
 	private TaxonVariant findHomoSapiensTV() {
 		Collection<TaxonVariant> hSap = getTaxonLabelHome().findTaxonVariantByFullName("Homo sapiens");
 		if (hSap == null) return null;
 		if (hSap.isEmpty()) return null;
 		return hSap.iterator().next();
 	}
+	
+
 }
 

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