X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=e812ed58c594ad5c3e890ab872344351800f9869;hp=eb1030c3640b7d400586d6fa6600d76984aca7a4;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index eb1030c..e812ed5 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -314,7 +314,8 @@ public abstract class FeatureRendererModel
   }
 
   @Override
-  public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
+  public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+          int column)
   {
     /*
      * include features at the position provided their feature type is 
@@ -408,8 +409,8 @@ public abstract class FeatureRendererModel
         }
         if (groupDisplayed)
         {
-          Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
-                  true, group);
+          Set<String> types = asq.getFeatures()
+                  .getFeatureTypesForGroups(true, group);
           for (String type : types)
           {
             if (!allfeatures.contains(type)) // or use HashSet and no test?
@@ -488,6 +489,7 @@ public abstract class FeatureRendererModel
       }
     }
   }
+
   protected Boolean firing = Boolean.FALSE;
 
   /**
@@ -628,8 +630,9 @@ public abstract class FeatureRendererModel
    */
   public boolean showFeatureOfType(String type)
   {
-    return type == null ? false : (av.getFeaturesDisplayed() == null ? true
-            : av.getFeaturesDisplayed().isVisible(type));
+    return type == null ? false
+            : (av.getFeaturesDisplayed() == null ? true
+                    : av.getFeaturesDisplayed().isVisible(type));
   }
 
   @Override
@@ -707,15 +710,15 @@ public abstract class FeatureRendererModel
   }
 
   /**
-   * Sets the priority order for features, with the highest priority (displayed on
-   * top) at the start of the data array
+   * Sets the priority order for features, with the highest priority (displayed
+   * on top) at the start of the data array
    * 
    * @param data
    *          an array of { Type, Colour, Filter, Boolean }
    * @param visibleNew
    *          when true current featureDisplay list will be cleared
-   * @return true if any visible features have been reordered or recoloured, else
-   *         false (i.e. no need to repaint)
+   * @return true if any visible features have been reordered or recoloured,
+   *         else false (i.e. no need to repaint)
    */
   public boolean setFeaturePriority(FeatureSettingsBean[] data,
           boolean visibleNew)
@@ -999,8 +1002,7 @@ public abstract class FeatureRendererModel
    */
   public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
   {
-    return featureGroups != null
-            && sequenceFeature.featureGroup != null
+    return featureGroups != null && sequenceFeature.featureGroup != null
             && sequenceFeature.featureGroup.length() != 0
             && featureGroups.containsKey(sequenceFeature.featureGroup)
             && !featureGroups.get(sequenceFeature.featureGroup)
@@ -1028,9 +1030,9 @@ public abstract class FeatureRendererModel
     List<String> visibleFeatures = getDisplayedFeatureTypes();
     String[] visibleTypes = visibleFeatures
             .toArray(new String[visibleFeatures.size()]);
-    List<SequenceFeature> features = sequence.getFeatures().findFeatures(
-            fromResNo, toResNo, visibleTypes);
-  
+    List<SequenceFeature> features = sequence.getFeatures()
+            .findFeatures(fromResNo, toResNo, visibleTypes);
+
     for (SequenceFeature sf : features)
     {
       if (!featureGroupNotShown(sf) && getColour(sf) != null)
@@ -1090,8 +1092,7 @@ 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()))
@@ -1121,7 +1122,8 @@ public abstract class FeatureRendererModel
   }
 
   @Override
-  public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
+  public void setFeatureFilter(String featureType,
+          FeatureMatcherSetI filter)
   {
     if (filter == null || filter.isEmpty())
     {
@@ -1159,7 +1161,7 @@ public abstract class FeatureRendererModel
     {
       return null;
     }
-  
+
     return fc.getColor(sf);
   }
 
@@ -1250,8 +1252,8 @@ public abstract class FeatureRendererModel
         int fromRes = match.getStart();
         int toRes = match.getEnd();
         mapFrom = match.getSequence();
-        List<SequenceFeature> fs = findFeaturesAtResidue(
-                mapFrom, fromRes, toRes);
+        List<SequenceFeature> fs = findFeaturesAtResidue(mapFrom, fromRes,
+                toRes);
         for (SequenceFeature sf : fs)
         {
           if (!found.contains(sf))
@@ -1296,8 +1298,9 @@ public abstract class FeatureRendererModel
         }
       }
     }
-    
-    return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
+
+    return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue,
+            result);
   }
 
   @Override