Merge: 497958b 68dcaa7

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3fedb92..a2da591 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -38,7 +38,6 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
-import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
@@ -447,7 +446,9 @@ public abstract class AlignmentViewport implements AlignViewportI
           AlignmentAnnotation alignmentAnnotation)
   {
     if (!alignmentAnnotation.autoCalculated)
+    {
       return false;
+    }
     if (calculator.workingInvolvedWith(alignmentAnnotation))
     {
       // System.err.println("grey out ("+alignmentAnnotation.label+")");
@@ -900,11 +901,12 @@ 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;
@@ -919,7 +921,8 @@ 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)
     {
@@ -929,9 +932,10 @@ 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)
@@ -965,12 +969,30 @@ 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();
@@ -1692,5 +1714,44 @@ public abstract class AlignmentViewport implements AlignViewportI
     return showSeqFeaturesHeight;
   }
 
+  private boolean showAnnotation = true;
+
+  private boolean rightAlignIds = false;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowAnnotation()
+  {
+    return isShowAnnotation();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
+
+  public boolean isShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
 
 }