X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=50a90fee2685a166a53eea56aa0a2d04a6d66f58;hb=65f3b4a9eadadb7540c329e710bce082ea1dd8a7;hp=51478f22f04a367394e66acf9f4c36762d364b72;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 51478f2..50a90fe 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,7 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showFullId = true;
+  boolean showJVSuffix = true;
   boolean showText = true;
   boolean showColourText = false;
   boolean showBoxes = true;
@@ -57,8 +57,7 @@ public class AlignViewport
 
   int charHeight;
   int charWidth;
-  int chunkWidth;
-  int chunkHeight;
+  int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
   AlignmentI alignment;
@@ -74,6 +73,17 @@ 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);
@@ -88,7 +98,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");
       if (param != null)
       {
-        showFullId = Boolean.valueOf(param).booleanValue();
+        showJVSuffix = Boolean.valueOf(param).booleanValue();
       }
 
       param = applet.getParameter("showAnnotation");
@@ -136,15 +146,12 @@ 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()
   {
+    if(alignment.isNucleotide())
+          return;
+
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
@@ -214,7 +221,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             1);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -224,7 +231,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        1);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -264,18 +271,21 @@ 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);
 
@@ -284,7 +294,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, 1);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
@@ -295,6 +305,9 @@ public class AlignViewport
       consensus.annotations = annotations;
     }
 
+    if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
+
   }
 
   public SequenceGroup getSelectionGroup()
@@ -429,24 +442,14 @@ public class AlignViewport
     return charHeight;
   }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
-
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
-
-  public void setChunkHeight(int h)
+  public void setWrappedWidth(int w)
   {
-    this.chunkHeight = h;
+    this.wrappedWidth = w;
   }
 
-  public int getChunkHeight()
+  public int getwrappedWidth()
   {
-    return chunkHeight;
+    return wrappedWidth;
   }
 
   public AlignmentI getAlignment()
@@ -593,14 +596,14 @@ public class AlignViewport
     return colourAppliesToAllGroups;
   }
 
-  public boolean getShowFullId()
+  public boolean getShowJVSuffix()
   {
-    return showFullId;
+    return showJVSuffix;
   }
 
-  public void setShowFullId(boolean b)
+  public void setShowJVSuffix(boolean b)
   {
-    showFullId = b;
+    showJVSuffix = b;
   }
 
   public boolean getShowAnnotation()
@@ -643,4 +646,58 @@ 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;
+  }
+
+
 }