Changeset 4442

Timestamp:

Mar 13, 2013, 2:09:13 PM (10 years ago)

Author:

marianne

Message:

Refs #774. Subgroup bugfix.

File:

• trunk/plugin/src/org/proteios/plugins/FeatureSequencePropagator.java (modified) (6 diffs)

trunk/plugin/src/org/proteios/plugins/FeatureSequencePropagator.java

@@ -743 +743 @@
           }
           
-          Set<Integer> maxSet = fileMatchMap.keySet();
+          Set<Integer> maxSet = new TreeSet<Integer>();
+          maxSet.addAll(fileMatchMap.keySet());
           Set<Integer> firstSubSet = fileMatchMap.get(0);
           Set<Integer> secondSubSet = fileMatchMap.get(0);
@@ -871 +872 @@
                 .getSecondFile());
             
-            if (addedSetAlignment && firstSubSet.contains(fp.getFirstFile()) && secondSubSet.contains(fp.getSecondFile()) && addedSetMatches<MATCHED_FILES_LIMIT || ((nbrMatchesPerFile[firstFileIndex]<currentMatch || nbrMatchesPerFile[secondFileIndex]<currentMatch) && nbrMatchesPerFile[firstFileIndex]<MATCHED_FILES_LIMIT+1 && nbrMatchesPerFile[secondFileIndex]<MATCHED_FILES_LIMIT+1)) { 
+            if (addedSetAlignment && firstSubSet.contains(fp.getFirstFile()) && secondSubSet.contains(fp.getSecondFile()) && addedSetMatches<MATCHED_FILES_LIMIT || ((nbrMatchesPerFile[firstFileIndex]<currentMatch || nbrMatchesPerFile[secondFileIndex]<currentMatch) && nbrMatchesPerFile[firstFileIndex]<MATCHED_FILES_LIMIT+1 && nbrMatchesPerFile[secondFileIndex]<MATCHED_FILES_LIMIT+1 && !breakAlignment)) {  
               
               if (addedSetAlignment){
-                
                 addedSetMatches++;
               }
               
-              if (addedSetMatches==MATCHED_FILES_LIMIT){
-                writer.println("Subgroups have matched " +(addedSetMatches-1) +"times." );
+              if (addedSetMatches==MATCHED_FILES_LIMIT || !itr.hasNext()){
                 addedSetAlignment = false;
               }
@@ -911 +910 @@
               writer.println();
               
-              hasMatchedAllFiles=setMatchedFiles(fp.getFirstFile(), fp.getSecondFile(), fileMatchMap, nbrOfFiles, writer);
+              hasMatchedAllFiles=setMatchedFiles(fp.getFirstFile(), fp.getSecondFile(), fileMatchMap, nbrOfFiles);
 
               // Alignment is to be performed, the matching
@@ -1087 +1086 @@
 
               }
-            }
+            
 
             
             if (breakAlignment) {
-              
-              if (hasMatchedAllFiles && !addedSetAlignment){
-                
+
+
+
+              if (hasMatchedAllFiles){
+
                 simList.clear();
                 break;
-                
+
               }else{
                 //there are subgroups of files that have not matched to each other
+                
+                writer.println();
+                writer.println("===============================");
+                writer.println();
+                
                 writer.println("There are subgroups in data.");
+                writer.println("Extending alignment between subgroups.");
                 
                 addedSetAlignment = true;
-                
+
                 firstSubSet = fileMatchMap.get(0);
-                writer.println("First subgroup: " +firstSubSet.toString());
-                
+
                 maxSet.removeAll(firstSubSet);
                 secondSubSet = new TreeSet<Integer>(maxSet);
-                writer.println("Other subgroup: " +secondSubSet.toString());
-                
-                maxSet = fileMatchMap.keySet();
+
+                maxSet.addAll(firstSubSet);
                 itr = simList.listIterator();
                 continue;
-                
+
+
               }
-              
-              
-              
-            }
-            
-            if(!addedSetAlignment){
+
+
+
+            }
+            
+            
               for (int ii = 0; ii < nbrMatchesPerFile.length; ii++) {
                 if (nbrMatchesPerFile[ii]<currentMatch) {
@@ -1467 +1473 @@
   }
   
-  private boolean setMatchedFiles(int file1, int file2, TreeMap<Integer, TreeSet<Integer>> fileMatchMap, int nbrOfFiles, PrintWriter writer){
+  private boolean setMatchedFiles(int file1, int file2, TreeMap<Integer, TreeSet<Integer>> fileMatchMap, int nbrOfFiles){
     
     Set<Integer> firstFileSet = fileMatchMap.get(file1);
@@ -1491 +1497 @@
     for(Integer key:secondFileSet){
       fileMatchMap.put(key, combinedSet);
-    }
-    
-    writer.println("Current map.");
-    for (int i=0; i<nbrOfFiles;i++){
-      writer.println(i +" " +fileMatchMap.get(i).toString());
-      
     }