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
{
/**
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
{
}
@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();
{
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())
// 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]);
}
{
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]))
{
}
else
{
- av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+ av.setFeaturesDisplayed(
+ av_featuresdisplayed = new FeaturesDisplayed());
}
}
else
{
// 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)
{