From a300ed430003b3c0af3f1badee464c0f40de63a0 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 17 Nov 2014 13:26:47 +0000
Subject: [PATCH] JAL-1293 hide/show sequence annotations with hide/reveal
 sequences

---
 src/jalview/datamodel/HiddenSequences.java   |   22 ++++++++-------
 src/jalview/viewmodel/AlignmentViewport.java |   37 ++++++++++++++++++++------
 2 files changed, 41 insertions(+), 18 deletions(-)

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index aefb5cc..bfeafd6 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -20,7 +20,9 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 public class HiddenSequences
 {
@@ -143,34 +145,34 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);
   }
 
-  public Vector showAll(
+  public List<SequenceI> showAll(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    Vector revealedSeqs = new Vector();
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
       {
-        Vector tmp = showSequence(i, hiddenRepSequences);
-        for (int t = 0; t < tmp.size(); t++)
+        List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+        for (SequenceI seq : tmp)
         {
-          revealedSeqs.addElement(tmp.elementAt(t));
+          revealedSeqs.add(seq);
         }
       }
     }
     return revealedSeqs;
   }
 
-  public Vector showSequence(int alignmentIndex,
+  public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    Vector revealedSeqs = new Vector();
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if (repSequence != null && hiddenRepSequences != null
             && hiddenRepSequences.containsKey(repSequence))
     {
       hiddenRepSequences.remove(repSequence);
-      revealedSeqs.addElement(repSequence);
+      revealedSeqs.add(repSequence);
     }
 
     int start = adjustForHiddenSeqs(alignmentIndex - 1);
@@ -192,7 +194,7 @@ public class HiddenSequences
         {
           if (seq.getLength() > 0)
           {
-            revealedSeqs.addElement(seq);
+            revealedSeqs.add(seq);
             asequences.add(alignmentIndex, seq);
           }
           else
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();
-- 
1.7.10.2