AlignPanel RefreshPanels put into paintComponent

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 166ab73..b07dce8 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -339,7 +339,6 @@ public class PopupMenu extends JPopupMenu
     if( superG !=null)\r
       superG.setSuperGroupProperties( sg );\r
 \r
-    ap.seqPanel.seqCanvas.paintFlag=true;\r
     ap.seqPanel.repaint();\r
   }\r
 \r
@@ -396,22 +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
@@ -435,7 +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
@@ -459,13 +464,14 @@ else // remove PIDColouring
                                           ap.av.alignment.getWidth());\r
 \r
         c.calculate();\r
-        c.verdict(false, 100);\r
+        c.verdict(false, ap.av.ConsPercGaps);\r
         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
 \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
@@ -540,7 +546,7 @@ else // remove PIDColouring
     if(s!=null)\r
     {\r
       sequence.setName(s);\r
-      ap.RefreshPanels();\r
+      ap.repaint();\r
     }\r
 \r
   }\r
@@ -550,7 +556,7 @@ else // remove PIDColouring
      SequenceGroup sg = ap.av.getSelectionGroup();\r
      ap.av.alignment.deleteGroup(sg);\r
      ap.av.setSelectionGroup(null);\r
-     ap.RefreshPanels();\r
+     ap.repaint();\r
   }\r
 \r
   void pdbMenuItem_actionPerformed(ActionEvent e)\r