modified history for redundancy removal.

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 610426f..fe03a31 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -100,6 +100,10 @@ public class AlignViewport
     if(Preferences.defaultColour!=null)\r
     {\r
       globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);\r
+      if(globalColourScheme instanceof UserColourScheme)\r
+      {\r
+        globalColourScheme = UserDefinedColours.loadDefaultColours();\r
+      }\r
       if(globalColourScheme!=null)\r
         globalColourScheme.setConsensus( vconsensus );\r
    }\r
@@ -156,7 +160,7 @@ public class AlignViewport
       float vprop = value-min;\r
       vprop/=max;\r
       annotations[i] = new Annotation(sequence.charAt(i) + "",\r
-                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+                                      "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
       // Quality calc\r
       value = ((Double) cons.quality.get(i)).floatValue();\r
       vprop = value - qmin;\r
@@ -308,7 +312,7 @@ public class AlignViewport
   }\r
   public void setEndRes(int res) {\r
     if (res > alignment.getWidth()-1) {\r
-      System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
        res = alignment.getWidth()-1;\r
     }\r
     if (res < 0) {\r
@@ -479,14 +483,10 @@ public class AlignViewport
   }\r
 \r
   public boolean getShowAnnotation()\r
-  {\r
-    return showAnnotation;\r
-  }\r
+  {   return showAnnotation;  }\r
 \r
   public void setShowAnnotation(boolean b)\r
-  {\r
-    showAnnotation = b;\r
-  }\r
+  {    showAnnotation = b;  }\r
 \r
   public boolean getScaleAboveWrapped()\r
   { return scaleAboveWrapped;}\r