From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 26 Jan 2015 16:45:29 +0000 (+0000)
Subject: Merge branch 'features/JAL-1588saveChimeraSession' into develop
X-Git-Tag: Jalview_2_9~106
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=c0aaf84826ff25d510846bd1099e10809c4df711

Merge branch 'features/JAL-1588saveChimeraSession' into develop
---

c0aaf84826ff25d510846bd1099e10809c4df711
diff --cc src/jalview/appletgui/AppletJmol.java
index 322a60f,0db3e30..4dcb5d7
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@@ -519,10 -552,12 +552,12 @@@ public class AppletJmol extends Embmenu
      else if (evt.getSource() == seqColour)
      {
        setEnabled(seqColour);
 -      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 +      jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
      }
      else if (!allChainsSelected)
+     {
        centerViewer();
+     }
    }
  
    public void keyPressed(KeyEvent evt)
diff --cc src/jalview/gui/AppJmolBinding.java
index 42a2f74,131f5bb..b7617ce
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@@ -50,15 -49,13 +49,13 @@@ public class AppJmolBinding extends Jal
      appJmolWindow = appJmol;
    }
  
-   FeatureRenderer fr = null;
- 
    @Override
-   public jalview.api.FeatureRenderer getFeatureRenderer(
+   public FeatureRenderer getFeatureRenderer(
            AlignmentViewPanel alignment)
    {
-     AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+     AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
              : (AlignmentPanel) alignment;
 -    if (ap.av.showSequenceFeatures)
 +    if (ap.av.isShowSequenceFeatures())
      {
        if (fr == null)
        {
@@@ -130,10 -127,12 +127,12 @@@
      AlignmentPanel ap = (AlignmentPanel) source, topap;
      // ignore events from panels not used to colour this view
      if (!appJmolWindow.isUsedforcolourby(ap))
+     {
        return;
+     }
      if (!isLoadingFromArchive())
      {
 -      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 +      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
      }
    }
  
diff --cc src/jalview/gui/JalviewChimeraBindingModel.java
index ece8856,a2a3184..0dcde11
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@@ -18,15 -20,13 +20,13 @@@ public class JalviewChimeraBindingMode
      cvf = chimeraViewFrame;
    }
  
-   FeatureRenderer fr = null;
- 
    @Override
-   public jalview.api.FeatureRenderer getFeatureRenderer(
+   public FeatureRenderer getFeatureRenderer(
            AlignmentViewPanel alignment)
    {
-     AlignmentPanel ap = (alignment == null) ? cvf.ap
+     AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
              : (AlignmentPanel) alignment;
 -    if (ap.av.showSequenceFeatures)
 +    if (ap.av.isShowSequenceFeatures())
      {
        if (fr == null)
        {
@@@ -71,9 -71,10 +71,10 @@@
      }
      if (!isLoadingFromArchive())
      {
 -      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 +      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
      }
    }
+ 
    @Override
    public void releaseReferences(Object svl)
    {