{
// TODO re JAL-860: optionally open dialog or provide a menu entry
// allowing user to open just one structure per sequence
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
- { pdb })[0], null, ap);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+ //{ pdb })[0], null, ap);
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(pdb,
+ ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe));
}
});
if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
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.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
+
+ AlignmentView selvew = ap.av.getAlignmentView(true, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.av
+ .getGapCharacter());
+ List<AlignmentAnnotation> ala = (ap.av
+ .getVisibleAlignmentAnnotation(true));
+ if (ala != null)
{
- for (int i = 0; i < nala.length; i++)
+ for (AlignmentAnnotation aa : ala)
{
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
+ aselview.addAnnotation(aa);
}
}
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+ aselview, null, null, null));
}
public void pdbFromFile_actionPerformed()
{ sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
"label.load_pdb_file_associate_with_sequence", new String[]
- { new Integer(sequence.getDisplayId(false)).toString() }));
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);