import java.awt.*;
import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.*;
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
public class AlignViewport implements SelectionSource, VamsasSource
{
{
if (alignment != null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager()
+ StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
.removeMappings(alignment.getCodonFrames());
}
this.alignment = align;
if (alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager().addMappings(
+ StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
alignment.getCodonFrames());
}
}
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sendSelection(
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()), this);
}
}
}
}
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb: pdbEntries) {
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ Vector pdbs = alignment.getSequenceAt(i)
+ .getDatasetSequence().getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq=alignment.getSequenceAt(i)))
+ seqs.add(sq);
+
+ continue;
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
}