X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=81d1b7ed34569490789c9bc3578c0b94e33bc69f;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=40f38b6eccbf6e56d063886d9f4203511b5d3826;hpb=7c70cb09e9de68ab567e38520d6d09f0c17a3939;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 40f38b6..81d1b7e 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -44,8 +44,8 @@ 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
 {
 
   /**
@@ -215,7 +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
       {
@@ -264,7 +265,8 @@ public abstract class FeatureRendererModel implements
   }
 
   @Override
-  public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+  public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence,
+          int res)
   {
     ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
@@ -273,15 +275,13 @@ public abstract class FeatureRendererModel implements
     {
       for (int i = 0; i < features.length; i++)
       {
-        if (!av.areFeaturesDisplayed()
-                || !av.getFeaturesDisplayed().isVisible(
-                        features[i].getType()))
+        if (!av.areFeaturesDisplayed() || !av.getFeaturesDisplayed()
+                .isVisible(features[i].getType()))
         {
           continue;
         }
 
-        if (features[i].featureGroup != null
-                && featureGroups != null
+        if (features[i].featureGroup != null && featureGroups != null
                 && featureGroups.containsKey(features[i].featureGroup)
                 && !featureGroups.get(features[i].featureGroup)
                         .booleanValue())
@@ -293,8 +293,8 @@ public abstract class FeatureRendererModel implements
         // lies between start and end
         if ((features[i].getBegin() == res || features[i].getEnd() == res)
                 || (!features[i].isContactFeature()
-                        && (features[i].getBegin() < res) && (features[i]
-                        .getEnd() >= res)))
+                        && (features[i].getBegin() < res)
+                        && (features[i].getEnd() >= res)))
         {
           tmp.add(features[i]);
         }
@@ -470,7 +470,8 @@ 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]))
           {
@@ -706,7 +707,8 @@ public abstract class FeatureRendererModel implements
       }
       else
       {
-        av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+        av.setFeaturesDisplayed(
+                av_featuresdisplayed = new FeaturesDisplayed());
       }
     }
     else
@@ -818,11 +820,12 @@ 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)
     {