JAL-1925 update source version in license

[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 a53004d..698c31e 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.viewmodel.seqfeatures;
 
 import jalview.api.AlignViewportI;
@@ -14,13 +34,11 @@ import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.Vector;
 import java.util.concurrent.ConcurrentHashMap;
 
 public abstract class FeatureRendererModel implements
@@ -121,8 +139,7 @@ public abstract class FeatureRendererModel implements
     }
     if (!fdi.isRegistered(featureType))
     {
-      pushFeatureType(Arrays.asList(new String[]
-      { featureType }));
+      pushFeatureType(Arrays.asList(new String[] { featureType }));
     }
     fdi.setVisible(featureType);
   }
@@ -165,7 +182,7 @@ public abstract class FeatureRendererModel implements
     types.toArray(neworder);
     if (renderOrder != null)
     {
-      System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+      System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
       System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
     }
     renderOrder = neworder;
@@ -188,8 +205,7 @@ public abstract class FeatureRendererModel implements
   protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
   {
     float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
-    final byte[] r = new byte[]
-    { 0, (byte) 255 };
+    final byte[] r = new byte[] { 0, (byte) 255 };
     if (mm != null)
     {
       if (r[0] != 0 || mm[0] < 0.0)
@@ -248,11 +264,12 @@ public abstract class FeatureRendererModel implements
   {
     ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
+
     if (features != null)
     {
       for (int i = 0; i < features.length; i++)
       {
-        if (av.areFeaturesDisplayed()
+        if (!av.areFeaturesDisplayed()
                 || !av.getFeaturesDisplayed().isVisible(
                         features[i].getType()))
         {
@@ -262,9 +279,11 @@ public abstract class FeatureRendererModel implements
         if (features[i].featureGroup != null
                 && featureGroups != null
                 && featureGroups.containsKey(features[i].featureGroup)
-                && !((Boolean) featureGroups.get(features[i].featureGroup))
+                && !featureGroups.get(features[i].featureGroup)
                         .booleanValue())
+        {
           continue;
+        }
 
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
@@ -322,9 +341,7 @@ public abstract class FeatureRendererModel implements
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       SequenceI asq = alignment.getSequenceAt(i);
-      SequenceI dasq = asq.getDatasetSequence();
-      SequenceFeature[] features = dasq != null ? dasq
-              .getSequenceFeatures() : asq.getSequenceFeatures();
+      SequenceFeature[] features = asq.getSequenceFeatures();
 
       if (features == null)
       {
@@ -345,7 +362,7 @@ public abstract class FeatureRendererModel implements
               groupDisplayed = Boolean.valueOf(newMadeVisible);
               featureGroups.put(fgrp, groupDisplayed);
             }
-            if (!((Boolean) groupDisplayed).booleanValue())
+            if (!groupDisplayed.booleanValue())
             {
               index++;
               continue;
@@ -370,20 +387,19 @@ public abstract class FeatureRendererModel implements
         {
           allfeatures.add(features[index].getType());
         }
-        if (features[index].score != Float.NaN)
+        if (!Float.isNaN(features[index].score))
         {
           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
           float[][] mm = (float[][]) minmax.get(features[index].getType());
           if (mm == null)
           {
-            mm = new float[][]
-            { null, null };
+            mm = new float[][] { null, null };
             minmax.put(features[index].getType(), mm);
           }
           if (mm[nonpos] == null)
           {
-            mm[nonpos] = new float[]
-            { features[index].score, features[index].score };
+            mm[nonpos] = new float[] { features[index].score,
+                features[index].score };
 
           }
           else
@@ -434,8 +450,7 @@ public abstract class FeatureRendererModel implements
         {
           if (initOrders)
           {
-            setOrder(oldRender[j], (1 - (1 + (float) j)
-                    / (float) oldRender.length));
+            setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
           }
           if (allfeatures.contains(oldRender[j]))
           {
@@ -666,9 +681,9 @@ public abstract class FeatureRendererModel implements
   }
 
   @Override
-  public Map getFeatureColours()
+  public Map<String, Object> getFeatureColours()
   {
-    return new ConcurrentHashMap<>(featureColours);
+    return featureColours;
   }
 
   /**
@@ -771,8 +786,7 @@ public abstract class FeatureRendererModel implements
   {
     if (renderOrder == null)
     {
-      return Arrays.asList(new String[]
-      {});
+      return Arrays.asList(new String[] {});
     }
     return Arrays.asList(renderOrder);
   }
@@ -799,7 +813,7 @@ public abstract class FeatureRendererModel implements
     }
     if (featureGroups.containsKey(group))
     {
-      return ((Boolean) featureGroups.get(group)).booleanValue();
+      return featureGroups.get(group).booleanValue();
     }
     if (newGroupsVisible)
     {
@@ -825,7 +839,7 @@ public abstract class FeatureRendererModel implements
 
       for (Object grp : featureGroups.keySet())
       {
-        Boolean state = (Boolean) featureGroups.get(grp);
+        Boolean state = featureGroups.get(grp);
         if (state.booleanValue() == visible)
         {
           gp.add(grp);
@@ -854,7 +868,7 @@ public abstract class FeatureRendererModel implements
         featureGroups.put(gst, new Boolean(visible));
         if (st != null)
         {
-          rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
+          rdrw = rdrw || (visible != st.booleanValue());
         }
       }
       if (rdrw)
@@ -900,7 +914,7 @@ public abstract class FeatureRendererModel implements
       {
         for (int i = 0; i < typ.length; i++)
         {
-          if (feature_disp.isVisible(typ[i]))
+          if (!feature_disp.isVisible(typ[i]))
           {
             typ[i] = null;
           }