featureGroups = fr.featureGroups;
featureColours = fr.featureColours;
transparency = fr.transparency;
- if (av!=null && fr.av!=null && fr.av!=av)
+ if (av != null && fr.av != null && fr.av != av)
{
- if (fr.av.featuresDisplayed!=null)
+ if (fr.av.featuresDisplayed != null)
{
- if (av.featuresDisplayed==null)
+ if (av.featuresDisplayed == null)
{
av.featuresDisplayed = new Hashtable();
- } else {
+ }
+ else
+ {
av.featuresDisplayed.clear();
}
- Enumeration en=fr.av.featuresDisplayed.keys();
+ Enumeration en = fr.av.featuresDisplayed.keys();
while (en.hasMoreElements())
{
av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceFeature[] features = alignment.getSequenceAt(i)
}
}
- ArrayList<String> hiddenGroups=new ArrayList<String>();
+ ArrayList<String> hiddenGroups = new ArrayList<String>();
+
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
{
featureGroups = new Hashtable();
}
- hiddenGroups =new ArrayList<String>();
+ hiddenGroups = new ArrayList<String>();
hiddenGroups.addAll(featureGroups.keySet());
ArrayList allFeatures = new ArrayList();
ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
if (alignment.getSequenceAt(i).getSequenceFeatures() == null)