treebase-guts

[Treebase-guts] SF.net SVN: treebase:[106] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/DownloadAStudyController.java

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

Revision: 106
          http://treebase.svn.sourceforge.net/treebase/?rev=106&view=rev
Author:   rvos
Date:     2009-06-25 02:40:49 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added RDF handling

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2009-06-25 02:40:12 UTC (rev 105)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2009-06-25 02:40:49 UTC (rev 106)
@@ -41,6 +41,9 @@
 		if ( getFormat(request) == FORMAT_NEXML ) {
 			return getNexmlService().serialize(study);
 		}
+		else if ( getFormat(request) == FORMAT_RDF ) {
+			return getRdfaService().serialize(study);			
+		}		
 		else {
 			StringBuilder builder = new StringBuilder();
 			builder.append("#NEXUS\n\n");


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[925] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/DownloadAStudyController.java

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

Revision: 925
          http://treebase.svn.sourceforge.net/treebase/?rev=925&view=rev
Author:   hshyket
Date:     2011-06-29 14:16:56 +0000 (Wed, 29 Jun 2011)

Log Message:
-----------
Fixing issue where TaxonLabelSet has a title of taxa.  Added a numeral to the taxon label set title.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2011-06-24 20:11:10 UTC (rev 924)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2011-06-29 14:16:56 UTC (rev 925)
@@ -48,8 +48,16 @@
 			// header:
 			TreebaseUtil.attachStudyHeader(study, builder);
 	
-			// taxa:			
+			// taxa:
+			
+			//set a unique number for each block when the title is Taxa
+			Integer taxa = 1;
 			for ( TaxonLabelSet tls : study.getTaxonLabelSets() ) {
+				if (tls.getTitle().equals("Taxa")) {
+					tls.setTitle(tls.getTitle() + taxa.toString());
+					taxa++;
+				}
+				
 				// one taxon label per line, no line number. 
 				tls.buildNexusBlockTaxa(builder, true, false);
 			}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[998] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/DownloadAStudyController.java

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

Revision: 998
          http://treebase.svn.sourceforge.net/treebase/?rev=998&view=rev
Author:   hshyket
Date:     2011-12-07 21:59:47 +0000 (Wed, 07 Dec 2011)
Log Message:
-----------
When downloading a study will loop through taxon block to check for duplicate blocks

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2011-12-06 21:59:41 UTC (rev 997)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2011-12-07 21:59:47 UTC (rev 998)
@@ -1,5 +1,8 @@
 package org.cipres.treebase.web.controllers;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -8,6 +11,7 @@
 import org.cipres.treebase.domain.matrix.Matrix;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelSet;
 import org.cipres.treebase.domain.tree.TreeBlock;
 import org.springframework.web.servlet.ModelAndView;
@@ -51,15 +55,35 @@
 			// taxa:
 			
 			//set a unique number for each block when the title is Taxa
-			Integer taxa = 1;
+			Integer taxaCount = 1;
+			List<List <TaxonLabel>> taxonCompare = new ArrayList<List <TaxonLabel>>();
 			for ( TaxonLabelSet tls : study.getTaxonLabelSets() ) {
-				if (tls.getTitle().equals("Taxa")) {
-					tls.setTitle(tls.getTitle() + taxa.toString());
-					taxa++;
+				Boolean isDuplicateTaxa = false;
+				Integer taxaCompareCount = 1;
+				
+				List<TaxonLabel> taxonLblSet = tls.getTaxonLabelsReadOnly();
+				if (taxonCompare != null) {
+					for (List<TaxonLabel> lstTls : taxonCompare) {
+						if (taxonLblSet.equals(lstTls)) {
+							isDuplicateTaxa = true;
+							break;
+						}
+						else {
+							taxaCompareCount++;
+						}
+					}
 				}
 				
-				// one taxon label per line, no line number. 
-				tls.buildNexusBlockTaxa(builder, true, false);
+				if (isDuplicateTaxa) {
+					tls.setTitle("Taxa" + taxaCompareCount.toString());
+				}
+				else {
+					tls.setTitle("Taxa" + taxaCount.toString());
+					taxaCount++;
+					// one taxon label per line, no line number. 
+					tls.buildNexusBlockTaxa(builder, true, false);
+					taxonCompare.add(taxonLblSet);
+				}
 			}
 			
 			// matrices::

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.