JAL-2374 fix popup out by one and multiple groups bugs

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 35ee8c4..90bdcae 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
@@ -365,17 +366,18 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
-  public SequenceGroup findGroup(SequenceI s)
+  public SequenceGroup findGroup(SequenceI seq, int position)
   {
     synchronized (groups)
     {
-      for (int i = 0; i < this.groups.size(); i++)
+      for (SequenceGroup sg : groups)
       {
-        SequenceGroup sg = groups.get(i);
-
-        if (sg.getSequences(null).contains(s))
+        if (sg.getSequences(null).contains(seq))
         {
-          return sg;
+          if (position >= sg.getStartRes() && position <= sg.getEndRes())
+          {
+            return sg;
+          }
         }
       }
     }
@@ -660,7 +662,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
-  public int findIndex(SearchResults results)
+  public int findIndex(SearchResultsI results)
   {
     int i = 0;
 
@@ -1054,6 +1056,7 @@ public class Alignment implements AlignmentI
   private void resolveAndAddDatasetSeq(SequenceI currentSeq,
           Set<SequenceI> seqs, boolean createDatasetSequence)
   {
+    SequenceI alignedSeq = currentSeq;
     if (currentSeq.getDatasetSequence() != null)
     {
       currentSeq = currentSeq.getDatasetSequence();
@@ -1088,12 +1091,19 @@ public class Alignment implements AlignmentI
         {
           if (dbr.getMap() != null && dbr.getMap().getTo() != null)
           {
+            if (dbr.getMap().getTo() == alignedSeq)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
             if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              throw new Error("Implementation error: Map.getTo() for dbref"
-                      + dbr + " is not a dataset sequence.");
-              // TODO: if this happens, could also rewrite the reference to
-              // point to new dataset sequence
+              throw new Error(
+                      "Implementation error: Map.getTo() for dbref " + dbr
+                              + " from " + curDs.getName()
+                              + " is not a dataset sequence.");
             }
             // we recurse to add all forward references to dataset sequences via
             // DBRefs/etc
@@ -1115,7 +1125,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1828,7 +1838,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**