X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=3606db90c85b9f438465aea2563ff4839d3c6f59;hb=fb27f86492eb06fc39b0578e1c31de8b4c26491a;hp=56a237bccb7c16af61d74c567297fe3c2d05b195;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 56a237b..3606db9 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,27 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+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
+public class AnnotationColourGradient extends FollowerColourScheme
 {
   public static final int NO_THRESHOLD = -1;
 
@@ -39,10 +47,32 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   float r1, g1, b1, rr, gg, bb, dr, dg, db;
 
-  ColourSchemeI colourScheme;
+  private boolean predefinedColours = false;
 
-  public boolean predefinedColours = false;
+  private boolean seqAssociated = false;
 
+  IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+    acg.thresholdIsMinMax = thresholdIsMinMax;
+    acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+    acg.r1 = r1;
+    acg.g1 = g1;
+    acg.b1 = b1;
+    acg.rr = rr;
+    acg.gg = gg;
+    acg.bb = bb;
+    acg.dr = dr;
+    acg.dg = dg;
+    acg.db = db;
+    acg.predefinedColours = predefinedColours;
+    acg.seqAssociated = seqAssociated;
+    
+    return acg;
+  }
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -92,6 +122,38 @@ 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>();
+      }
+      // resolve the context containing all the annotation for the sequence
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+      for (AlignmentAnnotation alan : alcontext.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;
@@ -114,11 +176,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
   }
 
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
   public Color getMinColour()
   {
     return new Color((int) r1, (int) g1, (int) b1);
@@ -152,13 +209,19 @@ 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
+      if (annotation.annotations!=null && j < annotation.annotations.length
               && annotation.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
@@ -182,14 +245,14 @@ 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);
@@ -202,9 +265,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j);
+            currentColour = colourScheme.findColour(c, j, seq);
           }
-          else if (range != 0)
+          else 
           {
             dr = rr * range + r1;
             dg = gg * range + g1;
@@ -223,4 +286,24 @@ 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;
+  }
 }