Conservation colour scheme is no more

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index f1ecd6a..6138257 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -491,7 +491,7 @@ public class AlignFrame
     sg.setEndRes(viewport.alignment.getWidth());\r
     viewport.setSelectionGroup(sg);\r
     alignPanel.repaint();\r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
@@ -499,7 +499,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);\r
     viewport.getColumnSelection().clear();\r
     viewport.setSelectionGroup(null);\r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
@@ -510,7 +510,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
     }\r
 \r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
@@ -808,21 +808,17 @@ public class AlignFrame
     {\r
       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 \r
-      if (cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-      }\r
+      cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
-    else if (cs instanceof ResidueColourScheme)\r
+    else\r
     {\r
-      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+      cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
     }\r
 \r
     if (viewport.getConservationSelected())\r
     {\r
-      ConservationColourScheme ccs = null;\r
 \r
       Alignment al = (Alignment) viewport.alignment;\r
       Conservation c = new Conservation("All",\r
@@ -833,13 +829,13 @@ public class AlignFrame
       c.calculate();\r
       c.verdict(false, viewport.ConsPercGaps);\r
 \r
-      ccs = new ConservationColourScheme(c, cs);\r
+      cs.setConservation(c);\r
 \r
       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
-      ccs.setConsensus(viewport.vconsensus);\r
-      viewport.setGlobalColourScheme(ccs);\r
+      cs.setConsensus(viewport.vconsensus);\r
+      viewport.setGlobalColourScheme(cs);\r
 \r
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
+      SliderPanel.setConservationSlider(alignPanel, cs, "Background");\r
 \r
     }\r
     else\r
@@ -885,10 +881,7 @@ public class AlignFrame
 \r
         if (viewport.getAbovePIDThreshold())\r
         {\r
-          if (sg.cs instanceof ResidueColourScheme)\r
-          {\r
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          }\r
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 \r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
         }\r
@@ -901,11 +894,10 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);\r
           c.calculate();\r
           c.verdict(false, viewport.ConsPercGaps);\r
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
-          sg.cs = ccs;\r
+          cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+          sg.cs = cs;\r
         }\r
         else\r
         {\r
@@ -959,15 +951,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);\r
     abovePIDThreshold.setState(false);\r
 \r
-    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-    if (cs instanceof ConservationColourScheme)\r
-    {\r
-      changeColour( ( (ConservationColourScheme) cs).cs);\r
-    }\r
-    else\r
-    {\r
-      changeColour(cs);\r
-    }\r
+    changeColour(viewport.getGlobalColourScheme());\r
 \r
     modifyConservation_actionPerformed(null);\r
   }\r
@@ -979,16 +963,7 @@ public class AlignFrame
     conservationMenuItem.setState(false);\r
     viewport.setConservationSelected(false);\r
 \r
-    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
-    if (cs instanceof ConservationColourScheme)\r
-    {\r
-      changeColour( ( (ConservationColourScheme) cs).cs);\r
-    }\r
-    else\r
-    {\r
-      changeColour(cs);\r
-    }\r
+    changeColour(viewport.getGlobalColourScheme());\r
 \r
     modifyPID_actionPerformed(null);\r
   }\r