JAL-2593 don't filter out 'colour by label' features

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 1af491c..231cfbe 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -26,6 +26,7 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.util.ColorUtils;
@@ -38,6 +39,7 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -262,10 +264,14 @@ public abstract class FeatureRendererModel implements
   }
 
   @Override
-  public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+  public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
+    /*
+     * include features at the position provided their feature type is 
+     * displayed, and feature group is null or marked for display
+     */
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    if (!av.areFeaturesDisplayed())
+    if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
     {
       return result;
     }
@@ -274,12 +280,7 @@ public abstract class FeatureRendererModel implements
             .getVisibleFeatures();
     String[] visibleTypes = visibleFeatures
             .toArray(new String[visibleFeatures.size()]);
-
-    /*
-     * include features at the position provided their feature type is 
-     * displayed, and feature group is null or marked for display
-     */
-    List<SequenceFeature> features = sequence.findFeatures(res, res,
+    List<SequenceFeature> features = sequence.findFeatures(column, column,
             visibleTypes);
 
     for (SequenceFeature sf : features)
@@ -558,7 +559,8 @@ public abstract class FeatureRendererModel implements
    * Returns the configured colour for a particular feature instance. This
    * includes calculation of 'colour by label', or of a graduated score colour,
    * if applicable. It does not take into account feature visibility or colour
-   * transparency.
+   * transparency. Returns null for a score feature whose score value lies
+   * outside any colour threshold.
    * 
    * @param feature
    * @return
@@ -570,19 +572,6 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * Answers true unless the feature has a graduated colour scheme and the
-   * feature value lies outside the current threshold for display
-   * 
-   * @param sequenceFeature
-   * @return
-   */
-  protected boolean showFeature(SequenceFeature sequenceFeature)
-  {
-    FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
-    return fc.isColored(sequenceFeature);
-  }
-
-  /**
    * Answers true if the feature type is currently selected to be displayed,
    * else false
    * 
@@ -966,4 +955,90 @@ public abstract class FeatureRendererModel implements
                     .booleanValue();
   }
 
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+          int resNo)
+  {
+    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
+    {
+      return result;
+    }
+
+    /*
+     * include features at the position provided their feature type is 
+     * displayed, and feature group is null or the empty string
+     * or marked for display
+     */
+    Set<String> visibleFeatures = getFeaturesDisplayed()
+            .getVisibleFeatures();
+    String[] visibleTypes = visibleFeatures
+            .toArray(new String[visibleFeatures.size()]);
+    List<SequenceFeature> features = sequence.getFeatures().findFeatures(
+            resNo, resNo, visibleTypes);
+  
+    for (SequenceFeature sf : features)
+    {
+      if (!featureGroupNotShown(sf))
+      {
+        result.add(sf);
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Removes from the list of features any that have a feature group that is not
+   * displayed, or duplicate the location of a feature of the same type (unless
+   * a graduated colour scheme or colour by label is applied). Should be used
+   * only for features of the same feature colour (which normally implies the
+   * same feature type).
+   * 
+   * @param features
+   * @param fc
+   */
+  public void filterFeaturesForDisplay(List<SequenceFeature> features,
+          FeatureColourI fc)
+  {
+    if (features.isEmpty())
+    {
+      return;
+    }
+    SequenceFeatures.sortFeatures(features, true);
+    boolean simpleColour = fc == null || fc.isSimpleColour();
+    SequenceFeature lastFeature = null;
+
+    Iterator<SequenceFeature> it = features.iterator();
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (featureGroupNotShown(sf))
+      {
+        it.remove();
+        continue;
+      }
+
+      /*
+       * a feature is redundant for rendering purposes if it has the
+       * same extent as another (so would just redraw the same colour);
+       * (checking type and isContactFeature as a fail-safe here, although
+       * currently they are guaranteed to match in this context)
+       */
+      if (simpleColour)
+      {
+        if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+                && sf.getEnd() == lastFeature.getEnd()
+                && sf.isContactFeature() == lastFeature.isContactFeature()
+                && sf.getType().equals(lastFeature.getType()))
+        {
+          it.remove();
+        }
+      }
+      lastFeature = sf;
+    }
+  }
+
 }