X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=2e79577e4a3d37656c60b940cab0c4f04acfc802;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=19c6ca889d50bcd6524a84b522cbda0b3e082002;hpb=0873fd1ab406be7ef121f466c7b53e4b6315bbca;p=jalview.git
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 19c6ca8..2e79577 100644
--- 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 2.9.0b1)
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.viewmodel.seqfeatures;
import jalview.api.AlignViewportI;
@@ -119,8 +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);
}
@@ -163,7 +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;
@@ -186,8 +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)
@@ -375,14 +393,13 @@ public abstract class FeatureRendererModel implements
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
@@ -433,8 +450,7 @@ 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]))
{
@@ -667,7 +683,7 @@ public abstract class FeatureRendererModel implements
@Override
public Map getFeatureColours()
{
- return new ConcurrentHashMap(featureColours);
+ return featureColours;
}
/**
@@ -770,8 +786,7 @@ public abstract class FeatureRendererModel implements
{
if (renderOrder == null)
{
- return Arrays.asList(new String[]
- {});
+ return Arrays.asList(new String[] {});
}
return Arrays.asList(renderOrder);
}