try
{
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (getViewport() != null)
- {
- configureFromViewport();
-
- }
int count = 0;
for (SequenceI seq : seqs)
this.displayedFeatures = displayedFeatures;
}
+ @Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ super.configureForView(avpanel);
+ if (isExporting())
+ {
+ setViewport(avpanel.getAlignViewport());
+ seqGroups = avpanel.getAlignment().getGroups();
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ fr = avpanel.cloneFeatureRenderer();
- setViewport(avpanel.getAlignViewport());
- seqGroups = avpanel.getAlignment().getGroups();
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- fr = avpanel.cloneFeatureRenderer();
+ for (SequenceI seq : getViewport().getAlignment().getSequences())
+ {
+ seqs.add(seq);
+ }
- for (SequenceI seq : getViewport().getAlignment().getSequences())
- {
- seqs.add(seq);
- }
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : getViewport().getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : getViewport().getAlignment()
+ .getAlignmentAnnotation())
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ annotations.add(annot);
}
- annotations.add(annot);
}
- }
- }
- public void configureFromViewport()
- {
- if (getViewport() == null)
- {
- return;
+ globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+ .getGlobalColourScheme());
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ showSeqFeatures = getViewport().isShowSequenceFeatures();
}
- globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
}
+
public static String getJSONData(AlignmentViewPanel av)
{
JSONFile jsonFile = new JSONFile();