IgnoreGapsConsensus

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 70608c4..5d94c3c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -523,6 +523,7 @@ public class Jalview2XML
         }\r
         catch (Exception ex)\r
         {\r
+          ex.printStackTrace();\r
             System.err.println("Exception whilst loading jalview XML file : " +\r
                 ex + "\n");\r
              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
@@ -631,11 +632,11 @@ public class Jalview2XML
 \r
                     if (cs instanceof ResidueColourScheme)\r
                     {\r
-                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);\r
                     }\r
                     else if (cs instanceof ScoreColourScheme)\r
                     {\r
-                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);\r
                     }\r
                 }\r
 \r
@@ -729,25 +730,28 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
             }\r
 \r
-            if (cs instanceof ConservationColourScheme)\r
-            {\r
-                ((ConservationColourScheme) cs).inc = view.getConsThreshold();\r
-            }\r
-\r
             if (cs instanceof ResidueColourScheme)\r
             {\r
-                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
+                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
             }\r
             else if (cs instanceof ScoreColourScheme)\r
             {\r
-                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
+                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
             }\r
+\r
+            if(cs!=null)\r
+              cs.setConsensus(af.viewport.vconsensus);\r
         }\r
 \r
+        af.setColourSelected(view.getBgColour());\r
         af.viewport.setGlobalColourScheme(cs);\r
-\r
         af.viewport.setColourAppliesToAllGroups(false);\r
         af.changeColour(af.viewport.getGlobalColourScheme());\r
+        if (view.getConservationSelected())\r
+        {\r
+          ( (ConservationColourScheme) af.viewport.getGlobalColourScheme()).inc = view.getConsThreshold();\r
+        }\r
+\r
         af.viewport.setColourAppliesToAllGroups(true);\r
 \r
         if (view.getShowSequenceFeatures())\r