IgnoreGapsConsensus

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 727e1c6..a41fb36 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1336,22 +1336,22 @@ public class AlignFrame extends GAlignFrame
 \r
             if (cs instanceof ResidueColourScheme)\r
             {\r
-                ((ResidueColourScheme) cs).setThreshold(threshold);\r
+                ((ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
             }\r
             else if (cs instanceof ScoreColourScheme)\r
             {\r
-                ((ScoreColourScheme) cs).setThreshold(threshold);\r
+                ((ScoreColourScheme) 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
         else if (cs instanceof ScoreColourScheme)\r
         {\r
-            ((ScoreColourScheme) cs).setThreshold(0);\r
+            ((ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
         }\r
 \r
         if (viewport.getConservationSelected())\r
@@ -1368,8 +1368,7 @@ public class AlignFrame extends GAlignFrame
 \r
             ccs = new ConservationColourScheme(c, cs);\r
 \r
-            // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
-            ccs.setConsensus(viewport.vconsensus);\r
+\r
             viewport.setGlobalColourScheme(ccs);\r
 \r
             ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
@@ -1421,11 +1420,11 @@ public class AlignFrame extends GAlignFrame
                 {\r
                     if (sg.cs instanceof ResidueColourScheme)\r
                     {\r
-                        ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+                        ((ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
                     }\r
                     else if (sg.cs instanceof ScoreColourScheme)\r
                     {\r
-                        ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+                        ((ScoreColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
                     }\r
 \r
                     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r