X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=78e850bacd01ba858e7357ab074005c8d8baa0a2;hb=bce28a70c870ff1283a8dd2720a7da69203039f0;hp=36c1f958e3a3a055a6a42c096d9683d1000ea81a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 36c1f95..78e850b 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,9 +17,15 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.IdentityHashMap;
+import java.util.Map;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
@@ -43,6 +49,10 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   public boolean predefinedColours = false;
 
+  public boolean seqAssociated = false;
+
+  IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -92,6 +102,33 @@ public class AnnotationColourGradient extends ResidueColourScheme
     bb = maxColour.getBlue() - b1;
   }
 
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO Auto-generated method stub
+    super.alignmentChanged(alignment, hiddenReps);
+    
+    if (seqAssociated && annotation.getCalcId() != null)
+    {
+      if (seqannot!=null) {
+        seqannot.clear();
+      } else {
+        seqannot=new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+      }
+      for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+              .getCalcId()))
+      {
+        if (alan.sequenceRef != null
+                && (alan.label != null && annotation != null && alan.label
+                        .equals(annotation.label)))
+        {
+          seqannot.put(alan.sequenceRef, alan);
+        }
+      }
+    }
+  }
+
   public String getAnnotation()
   {
     return annotation.label;
@@ -152,10 +189,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-
+    AlignmentAnnotation annotation=(seqAssociated ? seqannot.get(seq):this.annotation);
+    if (annotation==null)
+    {
+      return currentColour;
+    }
     if ((threshold == 0) || aboveThreshold(c, j))
     {
       if (j < annotation.annotations.length
@@ -202,7 +244,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j);
+            currentColour = colourScheme.findColour(c, j, seq);
           }
           else if (range != 0)
           {
@@ -223,4 +265,14 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
     return currentColour;
   }
+
+  public boolean isSeqAssociated()
+  {
+    return seqAssociated;
+  }
+
+  public void setSeqAssociated(boolean sassoc)
+  {
+    seqAssociated = sassoc;
+  }
 }