JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6ce68c3..9e5c4fb 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -35,6 +35,7 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;\r
 import jalview.datamodel.PDBEntry;\r
 import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceCollectionI;\r
 import jalview.datamodel.SequenceGroup;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.io.AnnotationFile;\r
@@ -2346,68 +2347,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }             \r
     viewport.setGlobalColourScheme(cs);\r
 \r
-    if (viewport.getColourAppliesToAllGroups())\r
-    {\r
-      Vector groups = viewport.getAlignment().getGroups();\r
-      for (int i = 0; i < groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
-        if (cs == null)\r
-        {\r
-          sg.cs = null;\r
-          continue;\r
-        }\r
-        if (cs instanceof ClustalxColourScheme)\r
-        {\r
-          sg.cs = new ClustalxColourScheme(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()),\r
-                  sg.getWidth());\r
-        }\r
-        else\r
-        {\r
-          try\r
-          {\r
-            sg.cs = cs.getClass().newInstance();\r
-          } catch (Exception ex)\r
-          {\r
-            ex.printStackTrace();\r
-            sg.cs = cs;\r
-          }\r
-        }\r
-\r
-        if (viewport.getAbovePIDThreshold()\r
-                || cs instanceof PIDColourScheme\r
-                || cs instanceof Blosum62ColourScheme)\r
-        {\r
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  sg.getWidth()));\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-        if (viewport.getConservationSelected())\r
-        {\r
-          Conservation c = new Conservation("Group",\r
-                  ResidueProperties.propHash, 3,\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  viewport.getAlignment().getWidth() - 1);\r
-          c.calculate();\r
-          c.verdict(false, viewport.getConsPercGaps());\r
-          sg.cs.setConservation(c);\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setConservation(null);\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-      }\r
-    }\r
 \r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r