X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cf6a901ec488015e62f8b67884740b7bccb97f81;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=514d486dc746582ae78b676c7d0d4d42ca1429f8;hpb=ca0a70b02a67f842a195319414d241ffa336656b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 514d486..cf6a901 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -845,7 +845,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
     conservationMenuItem.setEnabled(!nucleotide);
-    modifyConservation.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide
+            && conservationMenuItem.isSelected());
     showGroupConservation.setEnabled(!nucleotide);
 
     showComplementMenuItem.setText(nucleotide ? MessageManager
@@ -876,7 +877,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    modifyPID.setEnabled(abovePIDThreshold.isSelected());
     conservationMenuItem.setSelected(av.getConservationSelected());
+    modifyConservation.setEnabled(conservationMenuItem.isSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
     idRightAlign.setSelected(av.isRightAlignIds());
     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
@@ -1251,8 +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()));
@@ -1843,8 +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);
 
@@ -3297,11 +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);
   }
 
   /**
@@ -3343,19 +3345,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (cs != null)
     {
       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-      // Make sure viewport is up to date w.r.t. any sliders
-      if (viewport.getAbovePIDThreshold())
-      {
-        int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                "Background");
-        viewport.setThreshold(threshold);
-      }
-
-      if (viewport.getConservationSelected())
-      {
-        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
-                cs, "Background"));
-      }
     }
 
     viewport.setGlobalColourScheme(cs);
@@ -3364,77 +3353,71 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the PID threshold slider panel
    */
   @Override
   protected void modifyPID_actionPerformed()
   {
-    if (viewport.getAbovePIDThreshold()
-            && viewport.getGlobalColourScheme() != null)
-    {
-      SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
-      SliderPanel.showPIDSlider();
-    }
+    SliderPanel.setPIDSliderSource(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showPIDSlider();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the Conservation slider panel
    */
   @Override
   protected void modifyConservation_actionPerformed()
   {
-    if (viewport.getConservationSelected()
-            && viewport.getGlobalColourScheme() != null)
-    {
-      SliderPanel.setConservationSlider(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
-      SliderPanel.showConservationSlider();
-    }
+    SliderPanel.setConservationSlider(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showConservationSlider();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  protected void conservationMenuItem_actionPerformed()
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
+    viewport.getViewportColourScheme().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyConservation_actionPerformed();
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) Above PID Threshold
    */
   @Override
-  public void abovePIDThreshold_actionPerformed()
+  public void abovePIDThreshold_actionPerformed(boolean selected)
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
+    if (!selected)
+    {
+      viewport.getViewportColourScheme().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyPID_actionPerformed();
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   /**
@@ -4780,8 +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);
@@ -4851,6 +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
@@ -5689,17 +5693,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
 
-    /*
-     * select the default colour for the alignment (this may be
-     * overridden later)
-     */
-    boolean nucleotide = viewport.getAlignment().isNucleotide();
-    String defaultColourScheme = Cache.getDefault(
-            nucleotide ? Preferences.DEFAULT_COLOUR_NUC
-                    : Preferences.DEFAULT_COLOUR_PROT,
-            ResidueColourScheme.NONE);
+    ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+    String schemeName = colourScheme == null ? null : colourScheme
+            .getSchemeName();
 
-    ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
+    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
 }