pid and conservation changes

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d505ea..b04530c 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -395,22 +395,28 @@ public class PopupMenu extends JPopupMenu
 \r
   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
   {\r
-    if(abovePIDColour.isSelected())\r
-{\r
+    SequenceGroup sg = getGroup();\r
+    if (abovePIDColour.isSelected())\r
+    {\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+                                               ap.av.alignment.getWidth()));\r
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+      if (sg.cs instanceof ResidueColourScheme)\r
+        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+      else if (sg.cs instanceof ScoreColourScheme)\r
+        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 \r
-   Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
-   refresh();\r
-}\r
-else // remove PIDColouring\r
-{\r
-    ColourSchemeI cs = getGroup().cs;\r
-      ResidueColourScheme rcs = (ResidueColourScheme)cs;\r
-      rcs.setThreshold(0);\r
-      getGroup().cs = rcs;\r
-      refresh();\r
-}\r
+      SliderPanel.showPIDSlider();\r
 \r
+    }\r
+    else // remove PIDColouring\r
+    {\r
+      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
+      rcs.setThreshold(0);\r
+      sg.cs = rcs;\r
+    }\r
 \r
+    refresh();\r
 \r
   }\r
 \r
@@ -434,7 +440,7 @@ else // remove PIDColouring
 \r
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
   {\r
-    getGroup().cs = new Blosum62ColourScheme(ap.av);\r
+    getGroup().cs = new Blosum62ColourScheme();\r
     refresh();\r
   }\r
 \r
@@ -464,7 +470,8 @@ else // remove PIDColouring
 \r
       sg.cs = ccs;\r
 \r
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3bfc7db..0fa6d17 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -420,14 +420,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;\r
 \r
       if(av.getConservationSelected())\r
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())\r
-      {\r
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();\r
-        int threshold = rcs.getThreshold();\r
-        if (threshold > 0)\r
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
-      }\r
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
+      if(av.getAbovePIDThreshold())\r
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
 \r
     }\r
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
@@ -472,13 +467,9 @@ public class SeqPanel extends JPanel
 \r
     else if(stretchGroup.cs instanceof ConservationColourScheme)\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
-\r
-\r
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
        stretchGroup.cs = ccs;\r
-\r
-\r
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
 \r
        repaint();\r
     }\r
@@ -487,9 +478,7 @@ public class SeqPanel extends JPanel
       if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
       {\r
         ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;\r
-        int threshold = rcs.getThreshold();\r
-        if(threshold>0)\r
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
       }\r
 \r
     }\r