X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=e7cae4434305e6beea837c9fc87f28067a0db551;hb=9fff97021c2c637e426f6971d54dcf3fd4191985;hp=51478f22f04a367394e66acf9f4c36762d364b72;hpb=309f2ebc93eb5aab5478279a3c40914f216f01a4;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 51478f2..e7cae44 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -74,6 +74,9 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     setAlignment(al);
@@ -264,18 +267,21 @@ public class AlignViewport
     for (int i = 0; i < alignment.getWidth(); i++)
     {
       hash = (Hashtable) vconsensus.elementAt(i);
-      float value = new Float(hash.get("maxCount").toString()).floatValue();
-      value /= new Float(hash.get("size").toString()).floatValue();
+      float value = 0;
+      if(ignoreGapsInConsensusCalculation)
+        value = ((Float)hash.get("pid_nogaps")).floatValue();
+      else
+        value = ((Float)hash.get("pid_gaps")).floatValue();
 
-      value *= 100;
-      String maxRes = 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 + "%";
       annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
 
@@ -643,4 +649,24 @@ public class AlignViewport
     scaleRightWrapped = b;
   }
 
+  public void setIgnoreGapsConsensus(boolean b)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus();
+    if (globalColourScheme!=null && globalColourScheme instanceof ResidueColourScheme)
+    {
+      ( (ResidueColourScheme) globalColourScheme).setThreshold(
+          ( (ResidueColourScheme) globalColourScheme).getThreshold(),
+          ignoreGapsInConsensusCalculation);
+
+    }
+
+  }
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+
+
 }