JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5cc5111..cf6a901 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1254,8 +1254,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       FileFormatI format = fileFormat;
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
-              .formatSequences(format,
-                      exportData.getAlignment(),
+              .formatSequences(format, exportData.getAlignment(),
                       exportData.getOmitHidden(),
                       exportData.getStartEndPostions(),
                       viewport.getColumnSelection()));
@@ -1846,8 +1845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
-            seqs,
-            omitHidden, null);
+            seqs, omitHidden, null);
 
     StringSelection ss = new StringSelection(output);
 
@@ -3300,11 +3298,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * colour scheme to all groups. If unchecked, groups may have their own
    * independent colour schemes.
    * 
+   * @param selected
    */
   @Override
-  protected void applyToAllGroups_actionPerformed()
+  public void applyToAllGroups_actionPerformed(boolean selected)
   {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+    viewport.setColourAppliesToAllGroups(selected);
   }
 
   /**
@@ -3359,12 +3358,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void modifyPID_actionPerformed()
   {
-    if (viewport.getAbovePIDThreshold())
-    {
-      SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
-      SliderPanel.showPIDSlider();
-    }
+    SliderPanel.setPIDSliderSource(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showPIDSlider();
   }
 
   /**
@@ -3373,22 +3369,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void modifyConservation_actionPerformed()
   {
-    if (viewport.getConservationSelected()
-            && viewport.getGlobalColourScheme() != null)
-    {
-      SliderPanel.setConservationSlider(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
-      SliderPanel.showConservationSlider();
-    }
+    SliderPanel.setConservationSlider(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showConservationSlider();
   }
 
   /**
    * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  protected void conservationMenuItem_actionPerformed()
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
-    boolean selected = conservationMenuItem.isSelected();
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
     viewport.getViewportColourScheme().setConservationApplied(selected);
@@ -3408,11 +3399,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Action on selecting or deselecting (Colour) Above PID Threshold
    */
   @Override
-  public void abovePIDThreshold_actionPerformed()
+  public void abovePIDThreshold_actionPerformed(boolean selected)
   {
-    boolean selected = abovePIDThreshold.isSelected();
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
+    if (!selected)
+    {
+      viewport.getViewportColourScheme().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)
@@ -4768,8 +4763,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (FileFormat.Jnet.equals(format))
           {
-            JPredFile predictions = new JPredFile(
-                    file, sourceType);
+            JPredFile predictions = new JPredFile(file, sourceType);
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
@@ -4839,6 +4833,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     /*
+     * 'focus' any colour slider that is open to the selected viewport
+     */
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
+
+    /*
      * If there is a frame linked to this one in a SplitPane, switch it to the
      * same view tab index. No infinite recursion of calls should happen, since
      * tabSelectionChanged() should not get invoked on setting the selected