public void configureForView(AlignmentViewPanel avpanel)
{
super.configureForView(avpanel);
- if (isExporting())
- {
- setViewport(avpanel.getAlignViewport());
- seqGroups = avpanel.getAlignment().getGroups();
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- fr = avpanel.cloneFeatureRenderer();
- for (SequenceI seq : getViewport().getAlignment().getSequences())
- {
- seqs.add(seq);
- }
+ seqGroups = avpanel.getAlignment().getGroups();
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ fr = avpanel.cloneFeatureRenderer();
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : getViewport().getAlignment()
- .getAlignmentAnnotation())
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : getViewport().getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (annot != null && !annot.autoCalculated)
{
- if (annot != null && !annot.autoCalculated)
+ if (!annot.visible)
{
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- annotations.add(annot);
+ continue;
}
+ annotations.add(annot);
}
-
- 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();
- jsonFile.configureForView(av);
- String jsonString = jsonFile.print();
- return jsonString;
}
public boolean isShowSeqFeatures()