JAL-3383 JAL-3253-applet additional efficiencies; FeatureStore

[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 719cde4..8576482 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -988,10 +988,8 @@ public abstract class FeatureRendererModel
   {
     return featureGroups != null
             && sequenceFeature.featureGroup != null
-            && sequenceFeature.featureGroup.length() != 0
-            && featureGroups.containsKey(sequenceFeature.featureGroup)
-            && !featureGroups.get(sequenceFeature.featureGroup)
-                    .booleanValue();
+            && sequenceFeature.featureGroup.length() > 0 && featureGroups
+                    .get(sequenceFeature.featureGroup) == Boolean.FALSE;
   }
 
   /**
@@ -1030,11 +1028,11 @@ public abstract class FeatureRendererModel
   }
 
   /**
-   * Removes from the list of features any that duplicate the location of a
-   * feature of the same type. Should be used only for features of the same,
-   * simple, feature colour (which normally implies the same feature type). Does
-   * not check visibility settings for feature type or feature group. No
-   * filtering is done if transparency, or any feature filters, are in force.
+   * Removes from the list of features any whose group is not shown, or that are
+   * visible and duplicate the location of a visible feature of the same type.
+   * Should be used only for features of the same, simple, feature colour (which
+   * normally implies the same feature type). No filtering is done if
+   * transparency, or any feature filters, are in force.
    * 
    * @param features
    */
@@ -1058,6 +1056,11 @@ public abstract class FeatureRendererModel
     while (it.hasNext())
     {
       SequenceFeature sf = it.next();
+      if (featureGroupNotShown(sf))
+      {
+        it.remove();
+        continue;
+      }
 
       /*
        * a feature is redundant for rendering purposes if it has the
@@ -1065,7 +1068,8 @@ public abstract class FeatureRendererModel
        * (checking type and isContactFeature as a fail-safe here, although
        * currently they are guaranteed to match in this context)
        */
-      if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+      if (lastFeature != null
+              && sf.getBegin() == lastFeature.getBegin()
               && sf.getEnd() == lastFeature.getEnd()
               && sf.isContactFeature() == lastFeature.isContactFeature()
               && sf.getType().equals(lastFeature.getType()))
@@ -1177,4 +1181,32 @@ public abstract class FeatureRendererModel
   {
     Arrays.sort(renderOrder, order);
   }
+
+  @Override
+  public boolean isVisible(SequenceFeature feature)
+  {
+    if (feature == null)
+    {
+      return false;
+    }
+    if (getFeaturesDisplayed() == null
+            || !getFeaturesDisplayed().isVisible(feature.getType()))
+    {
+      return false;
+    }
+    if (featureGroupNotShown(feature))
+    {
+      return false;
+    }
+    FeatureColourI fc = featureColours.get(feature.getType());
+    if (fc != null && fc.isOutwithThreshold(feature))
+    {
+      return false;
+    }
+    if (!featureMatchesFilters(feature))
+    {
+      return false;
+    }
+    return true;
+  }
 }