patch for JAL-1300 fixes JAL-1294: read and write COMBINE statements that use SEQUENC...

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3d42475..b3a22df 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -131,7 +131,8 @@ public class AnnotationFile
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
       StringBuffer rowprops = new StringBuffer();
-      Hashtable graphGroup = new Hashtable();
+      Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
+      Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
       BitSet graphGroupSeen = new BitSet();
 
       java.awt.Color color;
@@ -147,54 +148,13 @@ public class AnnotationFile
 
         color = null;
         oneColour = true;
-
-        if (row.sequenceRef == null)
-        {
-          if (refSeq != null)
-          {
-            text.append(newline);
-            text.append("SEQUENCE_REF\tALIGNMENT");
-            text.append(newline);
-          }
-
-          refSeq = null;
-        }
-
-        else
-        {
-          if (refSeq == null || refSeq != row.sequenceRef)
-          {
-            refSeq = row.sequenceRef;
-            text.append(newline);
-            text.append("SEQUENCE_REF\t");
-            text.append(refSeq.getName());
-            text.append(newline);
-          }
-        }
+        
+        // mark any sequence references for the row
+        writeSequence_Ref(refSeq ,row.sequenceRef);
+        refSeq = row.sequenceRef;
         // mark any group references for the row
-        if (row.groupRef == null)
-        {
-
-          if (refGroup != null)
-          {
-            text.append(newline);
-            text.append("GROUP_REF\tALIGNMENT");
-            text.append(newline);
-          }
-
-          refGroup = null;
-        }
-        else
-        {
-          if (refGroup == null || refGroup != row.groupRef)
-          {
-            refGroup = row.groupRef;
-            text.append(newline);
-            text.append("GROUP_REF\t");
-            text.append(refGroup.getName());
-            text.append(newline);
-          }
-        }
+        writeGroup_Ref(refGroup, row.groupRef);
+        refGroup = row.groupRef;
 
         boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
         // lookahead to check what the annotation row object actually contains.
@@ -253,13 +213,15 @@ public class AnnotationFile
           if (row.graphGroup > -1)
           {
             graphGroupSeen.set(row.graphGroup);
-            String key = String.valueOf(row.graphGroup);
+            Integer key = new Integer(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
               graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+              
             }
             else
             {
+              graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
               graphGroup.put(key, row.label);
             }
           }
@@ -384,13 +346,26 @@ public class AnnotationFile
       text.append(graphLine.toString());
       if (graphGroup.size() > 0)
       {
-        Enumeration en = graphGroup.elements();
-        while (en.hasMoreElements())
-        {
+        SequenceI oldRefSeq = refSeq;
+        SequenceGroup oldRefGroup = refGroup;
+        for (Map.Entry<Integer, String> combine_statement:graphGroup.entrySet())
+        {
+          Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
+          
+          writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
+          refSeq = (SequenceI)seqRefAndGroup[0];
+          
+          writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
+          refGroup = (SequenceGroup)seqRefAndGroup[1];
           text.append("COMBINE\t");
-          text.append(en.nextElement());
+          text.append(combine_statement.getValue());
           text.append(newline);
         }
+        writeSequence_Ref(refSeq, oldRefSeq);
+        refSeq = oldRefSeq;
+        
+        writeGroup_Ref(refGroup, oldRefGroup);
+        refGroup = oldRefGroup;
       }
       text.append(rowprops.toString());
     }
@@ -421,6 +396,62 @@ public class AnnotationFile
     return text.toString();
   }
 
+  private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+  {
+    if (next_refGroup == null)
+    {
+
+      if (refGroup != null)
+      {
+        text.append(newline);
+        text.append("GROUP_REF\t");
+        text.append("ALIGNMENT");
+        text.append(newline);
+      }
+      return true;
+    }
+    else
+    {
+      if (refGroup == null || refGroup != next_refGroup)
+      {
+        text.append(newline);
+        text.append("GROUP_REF\t");
+        text.append(next_refGroup.getName());
+        text.append(newline);
+        return true;
+      }
+    }
+    return false;  
+  }
+  
+  private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+  {
+
+    if (next_refSeq==null)
+    {
+      if (refSeq != null)
+      {
+        text.append(newline);
+        text.append("SEQUENCE_REF\t");
+        text.append("ALIGNMENT");
+        text.append(newline);
+        return true;
+      }
+    }
+    else
+    {
+      if (refSeq == null || refSeq != next_refSeq)
+      {
+        text.append(newline);
+        text.append("SEQUENCE_REF\t");
+        text.append(next_refSeq.getName());
+        text.append(newline);
+        return true;
+      }
+    }
+    return false;
+  }
+
   public void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
@@ -594,10 +625,7 @@ public class AnnotationFile
           throws Exception
   {
     nlinesread = 0;
-    /**
-     * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
-     */
-    int combinecount = 0;
+    ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
     boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
@@ -683,7 +711,8 @@ public class AnnotationFile
 
         else if (token.equalsIgnoreCase("COMBINE"))
         {
-          combineAnnotations(al, combinecount++, st);
+          // keep a record of current state and resolve groupRef at end
+          combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
           modified = true;
           continue;
         }
@@ -898,7 +927,8 @@ public class AnnotationFile
         // and set modification flag
         modified = true;
       }
-      // Finally, resolve the groupRefs
+      // Resolve the groupRefs
+      Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
       Enumeration en = groupRefRows.keys();
 
       while (en.hasMoreElements())
@@ -922,6 +952,7 @@ public class AnnotationFile
             {
               matched = true;
               Vector rowset = (Vector) groupRefRows.get(groupRef);
+              groupRefLookup.put(groupRef,  theGroup);
               if (rowset != null && rowset.size() > 0)
               {
                 AlignmentAnnotation alan = null;
@@ -936,6 +967,20 @@ public class AnnotationFile
         }
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
+      // finally, combine all the annotation rows within each context.
+      /**
+       * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
+       */
+      int combinecount = 0;
+      for (Object[] _combine_args:combineAnnotation_calls) {
+        combineAnnotations(al, 
+                ++combinecount,
+                (StringTokenizer) _combine_args[0], // st
+                (SequenceI) _combine_args[1], // refSeq
+                (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
+                );
+      }
+
     }
     return modified;
   }
@@ -1092,7 +1137,7 @@ public class AnnotationFile
     }
   }
 
-  void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st)
+  void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
   {
     String group = st.nextToken();
     // First make sure we are not overwriting the graphIndex
@@ -1102,20 +1147,21 @@ public class AnnotationFile
       for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+        
         if (aa.graphGroup>graphGroup)
         {
           // try to number graphGroups in order of occurence.
-          graphGroup=aa.graphGroup;
+          graphGroup=aa.graphGroup+1;
         }
-        if (aa.label.equalsIgnoreCase(group))
+        if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
         {
           if (aa.graphGroup>-1)
           {
             graphGroup = aa.graphGroup;
           } else {
-            if (graphGroup >= combineCount)
+            if (graphGroup <= combineCount)
             {
-              graphGroup++;
+              graphGroup=combineCount+1;
             }
             aa.graphGroup = graphGroup;
           }
@@ -1129,9 +1175,10 @@ public class AnnotationFile
         group = st.nextToken();
         for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
-          if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+          AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+          if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
           {
-            al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+            aa.graphGroup = graphGroup;
             break;
           }
         }