Merge branch 'JAL-1403' into develop

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 6c46d0e..9c5512c 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -17,11 +17,17 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Map;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
@@ -43,7 +49,11 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   ColourSchemeI colourScheme;
 
-  public boolean predefinedColours = false;
+  private boolean predefinedColours = false;
+
+  private boolean seqAssociated = false;
+
+  IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   /**
    * Creates a new AnnotationColourGradient object.
@@ -94,6 +104,36 @@ 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;
@@ -158,7 +198,12 @@ public class AnnotationColourGradient extends ResidueColourScheme
   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
@@ -185,14 +230,14 @@ public class AnnotationColourGradient extends ResidueColourScheme
           if (thresholdIsMinMax
                   && annotation.threshold != null
                   && aboveAnnotationThreshold == ABOVE_THRESHOLD
-                  && annotation.annotations[j].value > annotation.threshold.value)
+                  && annotation.annotations[j].value >= annotation.threshold.value)
           {
             range = (annotation.annotations[j].value - annotation.threshold.value)
                     / (annotation.graphMax - annotation.threshold.value);
           }
           else if (thresholdIsMinMax && annotation.threshold != null
                   && aboveAnnotationThreshold == BELOW_THRESHOLD
-                  && annotation.annotations[j].value > annotation.graphMin)
+                  && annotation.annotations[j].value >= annotation.graphMin)
           {
             range = (annotation.annotations[j].value - annotation.graphMin)
                     / (annotation.threshold.value - annotation.graphMin);
@@ -207,7 +252,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
           {
             currentColour = colourScheme.findColour(c, j, seq);
           }
-          else if (range != 0)
+          else 
           {
             dr = rr * range + r1;
             dg = gg * range + g1;
@@ -226,4 +271,48 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
     return currentColour;
   }
+
+  public boolean isPredefinedColours()
+  {
+    return predefinedColours;
+  }
+
+  public void setPredefinedColours(boolean predefinedColours)
+  {
+    this.predefinedColours = predefinedColours;
+  }
+
+  public boolean isSeqAssociated()
+  {
+    return seqAssociated;
+  }
+
+  public void setSeqAssociated(boolean sassoc)
+  {
+    seqAssociated = sassoc;
+  }
+  @Override
+  public void setConsensus(Hashtable[] consensus)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConsensus(consensus);
+    }
+  }
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConservation(cons);
+    }
+  }
+  @Override
+  public void setConservationInc(int i)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConservationInc(i);
+    }
+  }
 }