X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f95179203d2bf94f45d5b4d2f0572c1838a32935;hb=c1d5d99668a2f897923f36234c8d86d14cf4f818;hp=05927b65851f11d35a01006e9b2d47697ec5c55b;hpb=d85d2bf55610bc799dd67d7f9ed6b494632e5420;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 05927b6..f951792 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -85,6 +85,8 @@ public class AlignViewport
     // JBPNote Prolly only need this in the applet version.
     private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
 
+    boolean ignoreGapsInConsensusCalculation = false;
+
     /**
      * Creates a new AlignViewport object.
      *
@@ -147,6 +149,7 @@ public class AlignViewport
             if (globalColourScheme instanceof UserColourScheme)
             {
                 globalColourScheme = UserDefinedColours.loadDefaultColours();
+                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
             }
 
             if (globalColourScheme != null)
@@ -304,18 +307,19 @@ public class AlignViewport
         {
             hash = (Hashtable) vconsensus.elementAt(i);
 
-            float value = Float.parseFloat(hash.get("maxCount").toString());
-            value /= Float.parseFloat(hash.get("size").toString());
-
-            value *= 100;
+            float value = 0;
+            if(ignoreGapsInConsensusCalculation)
+              value = ((Float)hash.get("pid_nogaps")).floatValue();
+            else
+              value = ((Float)hash.get("pid_gaps")).floatValue();
 
-            String maxRes = hash.get("maxResidue") + " ";
-            String mouseOver = hash.get("maxResidue") + " ";
+            String maxRes = hash.get("maxResidue").toString();
+            String mouseOver = hash.get("maxResidue")+" ";
 
-            if (maxRes.length() > 2)
+            if (maxRes.length() > 1)
             {
                 mouseOver = "[" + maxRes + "] ";
-                maxRes = "+ ";
+                maxRes = "+";
             }
 
             mouseOver += ((int) value + "%");
@@ -336,6 +340,9 @@ public class AlignViewport
         {
             consensus.annotations = annotations;
         }
+
+        if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
     }
 
     /**
@@ -995,7 +1002,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * Property change listener for changes in alignment
      *
      * @param listener DOCUMENT ME!
      */
@@ -1017,7 +1024,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * Property change listener for changes in alignment
      *
      * @param prop DOCUMENT ME!
      * @param oldvalue DOCUMENT ME!
@@ -1027,4 +1034,20 @@ public class AlignViewport
     {
         changeSupport.firePropertyChange(prop, oldvalue, newvalue);
     }
+
+    public void setIgnoreGapsConsensus(boolean b)
+    {
+      ignoreGapsInConsensusCalculation = b;
+      updateConsensus();
+      if(globalColourScheme!=null)
+      {
+        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+      }
+
+    }
+
+    public boolean getIgnoreGapsConsensus()
+    {
+     return ignoreGapsInConsensusCalculation;
+    }
 }