remove todo

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 78e850b..8f0626f 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,23 +1,25 @@
 /*
- * 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 2.8.0b1)
+ * 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 jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
@@ -27,7 +29,7 @@ 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;
 
@@ -45,14 +47,32 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   float r1, g1, b1, rr, gg, bb, dr, dg, db;
 
-  ColourSchemeI colourScheme;
-
-  public boolean predefinedColours = false;
+  private boolean predefinedColours = false;
 
-  public boolean seqAssociated = 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.
    */
@@ -106,17 +126,21 @@ public class AnnotationColourGradient extends ResidueColourScheme
   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) {
+      if (seqannot != null)
+      {
         seqannot.clear();
-      } else {
-        seqannot=new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
-      for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+      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
@@ -151,11 +175,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
   }
 
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
   public Color getMinColour()
   {
     return new Color((int) r1, (int) g1, (int) b1);
@@ -193,14 +212,15 @@ 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)
+    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))
       {
@@ -224,14 +244,14 @@ 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);
@@ -246,7 +266,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
           {
             currentColour = colourScheme.findColour(c, j, seq);
           }
-          else if (range != 0)
+          else 
           {
             dr = rr * range + r1;
             dg = gg * range + g1;
@@ -266,6 +286,16 @@ 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;