JAL-4071 colour rows according to simple/graduated feature colour, beginning of suppo...

diff --git a/examples/groovy/featuresCounter.groovy b/examples/groovy/featuresCounter.groovy
index dc4c97c..990800e 100644 (file)
--- a/examples/groovy/featuresCounter.groovy
+++ b/examples/groovy/featuresCounter.groovy
@@ -40,8 +40,8 @@ def annotator =
     [
      getNames: { ['Phosphorylation', 'Turn'] as String[] }, 
      getDescriptions:  { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] },
-     getMinColour: { [0, 255, 255] as int[] }, // cyan
-     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     getMinColour: {  i -> [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { i -> [0, 0, 255] as int[] }, // blue
      count: 
          { res, feats -> 
                 int phos

diff --git a/examples/groovy/visibleFeaturesCounter.groovy b/examples/groovy/visibleFeaturesCounter.groovy
index b3180f8..56b3912 100644 (file)
--- a/examples/groovy/visibleFeaturesCounter.groovy
+++ b/examples/groovy/visibleFeaturesCounter.groovy
@@ -75,8 +75,8 @@ def columnSetCounter =
     [
      getNames: { visibleFeatures as String[] }, 
      getDescriptions:  { visibleFeatures as String[] },
-     getMinColour: { [0, 255, 255] as int[] }, // cyan
-     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     getMinColour: { i-> [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { i-> [0, 0, 255] as int[] }, // blue
      count: 
          { res, feats -> 
              getCounts.call(feats) 

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 3a4bcc4..0858527 100644 (file)
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -29,6 +29,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureRenderer;
@@ -147,11 +148,6 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       max[crow] = 0;
     }
 
-    int[] minC = counter.getMinColour();
-    int[] maxC = counter.getMaxColour();
-    Color minColour = new Color(minC[0], minC[1], minC[2]);
-    Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
-
     for (int col = 0; col < width; col++)
     {
       int[] count = counts[col];
@@ -181,6 +177,11 @@ class ColumnCounterSetWorker extends AlignCalcWorker
 
     for (int anrow = 0; anrow < rows; anrow++)
     {
+      int[] minC = counter.getMinColour(anrow);
+      int[] maxC = counter.getMaxColour(anrow);
+      Color minColour = new Color(minC[0], minC[1], minC[2]);
+      Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
+
       Annotation[] anns = new Annotation[width];
       long rmax = 0;
       /*
@@ -276,6 +277,12 @@ class ColumnCounterSetWorker extends AlignCalcWorker
      */
     // see JAL-2075
     List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, col + 1);
+    if (fr.hasRenderOrder())
+    {
+      MappedFeatures mappedFeatres = fr.findComplementFeaturesAtResidue(seq,
+              seq.findPosition(col));
+      features.addAll(mappedFeatres.features);
+    }
     int[] count = this.counter.count(String.valueOf(res), features);
     return count;
   }

diff --git a/src/jalview/workers/FeatureSetCounterI.java b/src/jalview/workers/FeatureSetCounterI.java
index e14952f..fec8afd 100644 (file)
--- a/src/jalview/workers/FeatureSetCounterI.java
+++ b/src/jalview/workers/FeatureSetCounterI.java
@@ -21,10 +21,10 @@
 
 package jalview.workers;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.List;
 
+import jalview.datamodel.SequenceFeature;
+
 /**
  * An interface for a type that returns counts (per computed annotation type) of
  * any value of interest at a sequence position that can be determined from the
@@ -66,20 +66,22 @@ public interface FeatureSetCounterI
   String[] getDescriptions();
 
   /**
-   * Returns the colour (as [red, green, blue] values in the range 0-255) to use
-   * for the minimum value on histogram bars. If this is different to
-   * getMaxColour(), then bars will have a graduated colour.
+   * for each property returned from getNames Returns the colour (as [red,
+   * green, blue] values in the range 0-255) to use for the minimum value on
+   * histogram bars. If this is different to getMaxColour(), then bars will have
+   * a graduated colour.
    * 
    * @return
    */
-  int[] getMinColour();
+  int[] getMinColour(int anrow);
 
   /**
-   * Returns the colour (as [red, green, blue] values in the range 0-255) to use
-   * for the maximum value on histogram bars. If this is the same as
-   * getMinColour(), then bars will have a single colour (not graduated).
+   * for each property returned from getNames Returns the colour (as [red,
+   * green, blue] values in the range 0-255) to use for the maximum value on
+   * histogram bars. If this is the same as getMinColour(), then bars will have
+   * a single colour (not graduated).
    * 
    * @return
    */
-  int[] getMaxColour();
+  int[] getMaxColour(int anrow);
 }

diff --git a/src/jalview/workers/VisibleFeaturesAnnotationTracks.java b/src/jalview/workers/VisibleFeaturesAnnotationTracks.java
index baa8038..6e54628 100644 (file)
--- a/src/jalview/workers/VisibleFeaturesAnnotationTracks.java
+++ b/src/jalview/workers/VisibleFeaturesAnnotationTracks.java
@@ -20,14 +20,17 @@
  */
 package jalview.workers;
 
+import java.awt.Color;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.SequenceFeature;
 import jalview.gui.FeatureRenderer;
@@ -44,7 +47,10 @@ public class VisibleFeaturesAnnotationTracks implements FeatureSetCounterI
     @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
-      if (ourViewport != null) // could check source is
+      if (ourViewport != null) // could
+                               // check
+                               // source
+                               // is
                                // ourFr.getChangeSupport...
       {
         updateFeatureAnnotationTracks();
@@ -91,6 +97,9 @@ public class VisibleFeaturesAnnotationTracks implements FeatureSetCounterI
             .isShowSequenceFeatureCounts()
                     ? ourViewport.getFeaturesDisplayed()
                     : null;
+    // get latest FeatureRenderer, just in case it's different.
+    ourFr = ourFr.getAlignPanel().getFeatureRenderer();
+
     Set<String> visibleFeatures = new HashSet();
     if (featuresDisp != null)
     {
@@ -103,13 +112,35 @@ public class VisibleFeaturesAnnotationTracks implements FeatureSetCounterI
     }
     // otherwise set up tracks accordingly
 
+    int[][] minC = new int[visibleFeatures.size()][3],
+            maxC = new int[visibleFeatures.size()][3];
+    Map<String, FeatureColourI> fcs = ourFr.getDisplayedFeatureCols();
+    int p = 0;
+    for (String s : visibleFeatures)
+    {
+      FeatureColourI color = fcs.get(s);
+      if (color.isSimpleColour())
+      {
+        minC[p] = new int[] { 133, 133, 133 };
+        maxC[p] = new int[] { color.getColour().getRed(),
+            color.getColour().getGreen(), color.getColour().getBlue() };
+      }
+      else
+      {
+        Color min = color.getMinColour(), max = color.getMaxColour();
+        minC[p] = new int[] { min.getRed(), min.getGreen(), min.getBlue() };
+        maxC[p] = new int[] { max.getRed(), max.getGreen(), max.getBlue() };
+      }
+      p++;
+    }
+    minColours = minC;
+    maxColours = maxC;
     /*
      * and register the counter
      */
     if (ourWorker != null)
     {
-      Set<String> toRemove = new HashSet<String>(),
-              toAdd = new HashSet<String>();
+      Set<String> toRemove = new HashSet<String>();
       toRemove.addAll(dispFeatures);
       toRemove.removeAll(visibleFeatures);
       dispFeatures = visibleFeatures;
@@ -169,15 +200,25 @@ public class VisibleFeaturesAnnotationTracks implements FeatureSetCounterI
     return dispFeatures.toArray(new String[0]);
   }
 
+  int[][] minColours = null, maxColours = null;
+
   @Override
-  public int[] getMaxColour()
+  public int[] getMaxColour(int row)
   {
+    if (maxColours != null && row >= 0 && row < maxColours.length)
+    {
+      return maxColours[row];
+    }
     return new int[] { 0, 0, 255 };
   }
 
   @Override
-  public int[] getMinColour()
+  public int[] getMinColour(int row)
   {
-    return new int[] { 0, 255, 255 };
+    if (minColours != null && row >= 0 && row < minColours.length)
+    {
+      return minColours[row];
+    }
+    return new int[] { 133, 133, 133 };
   }
 }
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