X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=40d3dd499a51bb149c8ce4c70616cc70c16bd648;hb=8878681ec11f85c050248236a96ffbcaf2f0497b;hp=51478f22f04a367394e66acf9f4c36762d364b72;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 51478f2..40d3dd4 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -74,6 +74,17 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
+  public Vector vconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     setAlignment(al);
@@ -136,12 +147,6 @@ public class AlignViewport
     showSequenceFeatures = b;
   }
 
-  public Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
-
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
   public void updateConservation()
   {
@@ -264,18 +269,21 @@ 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);
 
@@ -295,6 +303,9 @@ public class AlignViewport
       consensus.annotations = annotations;
     }
 
+    if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
+
   }
 
   public SequenceGroup getSelectionGroup()
@@ -643,4 +654,58 @@ public class AlignViewport
     scaleRightWrapped = b;
   }
 
+  public void setIgnoreGapsConsensus(boolean b)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus();
+    if (globalColourScheme!=null)
+    {
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+          ignoreGapsInConsensusCalculation);
+
+    }
+  }
+
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void addPropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+      changeSupport.addPropertyChangeListener(listener);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void removePropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+      changeSupport.removePropertyChangeListener(listener);
+  }
+
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param prop DOCUMENT ME!
+   * @param oldvalue DOCUMENT ME!
+   * @param newvalue DOCUMENT ME!
+   */
+  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  {
+      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+  }
+
+
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+
+
 }