IgnoreGapsConsensus

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0bdcb55..db1f9c9 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -808,14 +808,14 @@ public class AlignFrame
 \r
       if (cs instanceof ResidueColourScheme)\r
       {\r
-        ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
       }\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
     else if (cs instanceof ResidueColourScheme)\r
     {\r
-      ( (ResidueColourScheme) cs).setThreshold(0);\r
+      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
     }\r
 \r
     if (viewport.getConservationSelected())\r
@@ -885,7 +885,7 @@ public class AlignFrame
         {\r
           if (sg.cs instanceof ResidueColourScheme)\r
           {\r
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
           }\r
 \r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
@@ -914,6 +914,8 @@ public class AlignFrame
       }\r
     }\r
 \r
+    updateCSConsensus();\r
+\r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r
       alignPanel.getOverviewPanel().updateOverviewImage();\r
@@ -922,6 +924,12 @@ public class AlignFrame
     alignPanel.repaint();\r
   }\r
 \r
+  public void updateCSConsensus()\r
+  {\r
+    //Colour schemes must have their consensus updated\r
+\r
+  }\r
+\r
   protected void modifyPID_actionPerformed(ActionEvent e)\r
   {\r
     if (viewport.getAbovePIDThreshold())\r