X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=1b42faf037a32f8ec693723f9c2d4c12a74abbd6;hb=a300ed430003b3c0af3f1badee464c0f40de63a0;hp=0fa4a3c55e05a15eae76b327e0a8d5be53a6e085;hpb=1aa21d01e983854e9dbb1628350ac6976c52430a;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0fa4a3c..1b42faf 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,7 +20,6 @@
  */
 package jalview.viewmodel;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
@@ -35,7 +34,6 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
@@ -447,7 +445,9 @@ public abstract class AlignmentViewport implements AlignViewportI
           AlignmentAnnotation alignmentAnnotation)
   {
     if (!alignmentAnnotation.autoCalculated)
+    {
       return false;
+    }
     if (calculator.workingInvolvedWith(alignmentAnnotation))
     {
       // System.err.println("grey out ("+alignmentAnnotation.label+")");
@@ -899,11 +899,12 @@ public abstract class AlignmentViewport implements AlignViewportI
         selectionGroup = new SequenceGroup();
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      Vector tmp = alignment.getHiddenSequences().showAll(
+      List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
               hiddenRepSequences);
-      for (int t = 0; t < tmp.size(); t++)
+      for (SequenceI seq : tmp)
       {
-        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+        selectionGroup.addSequence(seq, false);
+        setSequenceAnnotationsVisible(seq, true);
       }
 
       hasHiddenRows = false;
@@ -918,7 +919,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   public void showSequence(int index)
   {
-    Vector tmp = alignment.getHiddenSequences().showSequence(index,
+    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+            index,
             hiddenRepSequences);
     if (tmp.size() > 0)
     {
@@ -928,9 +930,10 @@ public abstract class AlignmentViewport implements AlignViewportI
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
 
-      for (int t = 0; t < tmp.size(); t++)
+      for (SequenceI seq : tmp)
       {
-        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+        selectionGroup.addSequence(seq, false);
+        setSequenceAnnotationsVisible(seq, true);
       }
       // JBPNote: refactor: only update flag if we modified visiblity (used to
       // do this regardless)
@@ -964,12 +967,30 @@ public abstract class AlignmentViewport implements AlignViewportI
       for (int i = 0; i < seq.length; i++)
       {
         alignment.getHiddenSequences().hideSequence(seq[i]);
+        setSequenceAnnotationsVisible(seq[i], false);
       }
       hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
 
+  /**
+   * Set visibility for any annotations for the given sequence.
+   * 
+   * @param sequenceI
+   */
+  protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+          boolean visible)
+  {
+    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    {
+      if (ann.sequenceRef == sequenceI)
+      {
+        ann.visible = visible;
+      }
+    }
+  }
+
   public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
   {
     int sSize = sg.getSize();