X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=2f30e9463a994ed8c7ad9d7eaa9b6260932551dc;hb=refs%2Fheads%2Fportforward%2FJAL-2675_2102b1to2103;hp=a568341e9bf984edd7cdf86401dda4480588bfd0;hpb=4c6cd08af580ff73cfce39bec34ae4658a4b4b34;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index a568341..2f30e94 100644
--- 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;
@@ -38,13 +39,14 @@ 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;
 import java.util.concurrent.ConcurrentHashMap;
 
-public abstract class FeatureRendererModel implements
-        jalview.api.FeatureRenderer
+public abstract class FeatureRendererModel
+        implements jalview.api.FeatureRenderer
 {
 
   /**
@@ -213,7 +215,8 @@ public abstract class FeatureRendererModel implements
       if (r[0] != 0 || mm[0] < 0.0)
       {
         r[0] = 1;
-        r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+        r[1] = (byte) ((int) 128.0
+                + 127.0 * (sequenceFeature.score / mm[1]));
       }
       else
       {
@@ -460,7 +463,8 @@ public abstract class FeatureRendererModel implements
         {
           if (initOrders)
           {
-            setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
+            setOrder(oldRender[j],
+                    (1 - (1 + (float) j) / oldRender.length));
           }
           if (allfeatures.contains(oldRender[j]))
           {
@@ -557,7 +561,8 @@ 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
@@ -569,19 +574,6 @@ 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
    * 
@@ -696,7 +688,8 @@ public abstract class FeatureRendererModel implements
       }
       else
       {
-        av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+        av.setFeaturesDisplayed(
+                av_featuresdisplayed = new FeaturesDisplayed());
       }
     }
     else
@@ -808,11 +801,12 @@ public abstract class FeatureRendererModel implements
   {
     // conflict between applet and desktop - featureGroups returns the map in
     // the desktop featureRenderer
-    return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
-            .asList(featureGroups.keySet().toArray(new String[0]));
+    return (featureGroups == null) ? Arrays.asList(new String[0])
+            : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
   }
 
-  public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+  public boolean checkGroupVisibility(String group,
+          boolean newGroupsVisible)
   {
     if (featureGroups == null)
     {
@@ -1000,4 +994,55 @@ public abstract class FeatureRendererModel implements
     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;
+    }
+  }
+
 }