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JAL-1645 source formatting and organise imports
[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
c7cee04
..
bedbaf5
100644
(file)
--- a/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@
-119,8
+119,7
@@
public abstract class FeatureRendererModel implements
}
if (!fdi.isRegistered(featureType))
{
}
if (!fdi.isRegistered(featureType))
{
- pushFeatureType(Arrays.asList(new String[]
- { featureType }));
+ pushFeatureType(Arrays.asList(new String[] { featureType }));
}
fdi.setVisible(featureType);
}
}
fdi.setVisible(featureType);
}
@@
-163,7
+162,7
@@
public abstract class FeatureRendererModel implements
types.toArray(neworder);
if (renderOrder != null)
{
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;
System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
}
renderOrder = neworder;
@@
-186,8
+185,7
@@
public abstract class FeatureRendererModel implements
protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
{
float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
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)
if (mm != null)
{
if (r[0] != 0 || mm[0] < 0.0)
@@
-247,12
+245,6
@@
public abstract class FeatureRendererModel implements
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
- while (features == null && sequence.getDatasetSequence() != null)
- {
- sequence = sequence.getDatasetSequence();
- features = sequence.getSequenceFeatures();
- }
-
if (features != null)
{
for (int i = 0; i < features.length; i++)
if (features != null)
{
for (int i = 0; i < features.length; i++)
@@
-329,9
+321,7
@@
public abstract class FeatureRendererModel implements
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
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)
{
if (features == null)
{
@@
-377,20
+367,19
@@
public abstract class FeatureRendererModel implements
{
allfeatures.add(features[index].getType());
}
{
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)
{
{
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)
{
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
}
else
@@
-441,8
+430,7
@@
public abstract class FeatureRendererModel implements
{
if (initOrders)
{
{
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]))
{
}
if (allfeatures.contains(oldRender[j]))
{
@@
-778,8
+766,7
@@
public abstract class FeatureRendererModel implements
{
if (renderOrder == null)
{
{
if (renderOrder == null)
{
- return Arrays.asList(new String[]
- {});
+ return Arrays.asList(new String[] {});
}
return Arrays.asList(renderOrder);
}
}
return Arrays.asList(renderOrder);
}