Merge branch 'features/JAL-2360colourSchemeApplicability' into

features/JAL-2371collectionColourScheme

Conflicts:
	src/jalview/appletgui/SliderPanel.java
	src/jalview/gui/SliderPanel.java

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 2aa010f..1beb82b 100644 (file)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -60,22 +60,21 @@ public class SliderPanel extends Panel implements ActionListener,
   static Frame PIDSlider;
 
   public static int setConservationSlider(AlignmentPanel ap,
-          CollectionColourSchemeI collectionColourSchemeI, String source)
+          CollectionColourSchemeI ccs, String source)
   {
     SliderPanel sp = null;
 
     if (conservationSlider == null)
     {
-      sp = new SliderPanel(ap,
-              collectionColourSchemeI.getConservationInc(), true,
-              collectionColourSchemeI);
+      sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
       conservationSlider = new Frame();
       conservationSlider.add(sp);
     }
     else
     {
       sp = (SliderPanel) conservationSlider.getComponent(0);
-      sp.cs = collectionColourSchemeI;
+      sp.cs = ccs;
+      sp.valueField.setText(String.valueOf(ccs.getConservationInc()));
     }
 
     conservationSlider
@@ -135,6 +134,7 @@ public class SliderPanel extends Panel implements ActionListener,
     {
       pid = (SliderPanel) PIDSlider.getComponent(0);
       pid.cs = ccs;
+      pid.valueField.setText(String.valueOf(ccs.getThreshold()));
     }
     PIDSlider
             .setTitle(MessageManager.formatMessage(

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 6b764d0..47b0694 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1739,7 +1739,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         SliderPanel.setConservationSlider(ap, groupColourScheme, name);
       }
-      else
+      if (stretchGroup.cs.getThreshold() > 0)
       {
         SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
       }

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index b386dec..4600ab7 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -118,7 +118,7 @@ public class SliderPanel extends GSliderPanel
    * 
    * @param ap
    *          DOCUMENT ME!
-   * @param cs
+   * @param ccs
    *          DOCUMENT ME!
    * @param source
    *          DOCUMENT ME!
@@ -126,13 +126,13 @@ public class SliderPanel extends GSliderPanel
    * @return DOCUMENT ME!
    */
   public static int setConservationSlider(AlignmentPanel ap,
-          CollectionColourSchemeI cs, String source)
+          CollectionColourSchemeI ccs, String source)
   {
     SliderPanel sp = null;
 
     if (conservationSlider == null)
     {
-      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+      sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
       conservationSlider = new JInternalFrame();
       conservationSlider.setContentPane(sp);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -140,8 +140,8 @@ public class SliderPanel extends GSliderPanel
     else
     {
       sp = (SliderPanel) conservationSlider.getContentPane();
-      sp.slider.setValue(cs.getConservationInc());
-      sp.cs = cs;
+      sp.valueField.setText(String.valueOf(ccs.getConservationInc()));
+      sp.cs = ccs;
     }
 
     conservationSlider
@@ -224,7 +224,7 @@ public class SliderPanel extends GSliderPanel
    * 
    * @param ap
    *          DOCUMENT ME!
-   * @param collectionColourScheme
+   * @param ccs
    *          DOCUMENT ME!
    * @param source
    *          DOCUMENT ME!
@@ -232,16 +232,15 @@ public class SliderPanel extends GSliderPanel
    * @return DOCUMENT ME!
    */
   public static int setPIDSliderSource(AlignmentPanel ap,
-          CollectionColourSchemeI collectionColourScheme,
-          String source)
+          CollectionColourSchemeI ccs, String source)
   {
     SliderPanel pid = null;
 
-    int threshold = collectionColourScheme.getThreshold();
+    int threshold = ccs.getThreshold();
 
     if (PIDSlider == null)
     {
-      pid = new SliderPanel(ap, threshold, false, collectionColourScheme);
+      pid = new SliderPanel(ap, threshold, false, ccs);
       PIDSlider = new JInternalFrame();
       PIDSlider.setContentPane(pid);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -249,8 +248,8 @@ public class SliderPanel extends GSliderPanel
     else
     {
       pid = (SliderPanel) PIDSlider.getContentPane();
-      pid.cs = collectionColourScheme;
-      pid.slider.setValue(collectionColourScheme.getThreshold());
+      pid.cs = ccs;
+      pid.valueField.setText(String.valueOf(ccs.getThreshold()));
     }
 
     PIDSlider