return null;
}
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(
- viewport.getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
else
{
- features = formatter.printGffFormat(
- viewport.getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printGffFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
if (displayTextbox)
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components
+ Vector comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
for (int i = 0; i < comps.size(); i++)
{
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components
+ Vector comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)