String[] omitHidden = null;
- if (ap.av.hasHiddenColumns)
- {
- System.out.println("PROMPT USER HERE");
- omitHidden = ap.av.getViewAsString(true);
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+ omitHidden = ap.av.getViewAsString(true);
+ Alignment oal = new Alignment(ap.av.getSequenceSelection());
+ AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+ for (int i=0; i<nala.length; i++)
+ {
+ AlignmentAnnotation na =nala[i];
+ oal.addAnnotation(na);
}
-
cap.setText(new FormatAdapter().formatSequences(
- e.getActionCommand(),
- ap.av.getSelectionAsNewSequence(),
- omitHidden));
+ e.getActionCommand(),
+ oal,
+ omitHidden, csel, sg));
+ oal=null;
}
public void pdbFromFile_actionPerformed()