import jalview.structure.StructureSelectionManager;
import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
/**
* proxy for handling structure viewers.
ssm = structureSelectionManager;
}
- public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
- PDBEntry[] pr, SequenceI[][] collateForPDB)
+ /**
+ * View multiple PDB entries, each with associated sequences
+ *
+ * @param pdbs
+ * @param seqsForPdbs
+ * @param ap
+ * @return
+ */
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
- return viewStructures(getViewerType(), ap, pr, collateForPDB);
+ JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqsForPdbs, ap);
+ if (viewer != null)
+ {
+ return viewer;
+ }
+ return viewStructures(getViewerType(), pdbs, seqsForPdbs, ap);
}
- public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+ /**
+ * A strictly temporary method pending JAL-1761 refactoring. Determines if all
+ * the passed PDB entries are the same (this is the case if selected sequences
+ * to view structure for are chains of the same structure). If so, calls the
+ * single-pdb version of viewStructures and returns the viewer, else returns
+ * null.
+ *
+ * @param pdbs
+ * @param seqsForPdbs
+ * @param ap
+ * @return
+ */
+ private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
+ SequenceI[][] seqsForPdbs, AlignmentPanel ap)
+ {
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ if (pdbs == null || pdbs.length == 0)
+ {
+ return null;
+ }
+ int i = 0;
+ String firstFile = pdbs[0].getFile();
+ for (PDBEntry pdb : pdbs)
+ {
+ String pdbFile = pdb.getFile();
+ if (pdbFile == null || !pdbFile.equals(firstFile))
+ {
+ return null;
+ }
+ SequenceI[] pdbseqs = seqsForPdbs[i++];
+ if (pdbseqs != null)
+ {
+ for (SequenceI sq : pdbseqs)
+ {
+ seqs.add(sq);
+ }
+ }
+ }
+ return viewStructures(pdbs[0],
+ seqs.toArray(new SequenceI[seqs.size()]), ap);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+ SequenceI[] seqsForPdb, AlignmentPanel ap)
+ {
+ return viewStructures(getViewerType(), pdb, seqsForPdb, ap);
+ }
+
+ protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs));
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+ sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
}
else
{
return sview;
}
- public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+ protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
{
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(pr, collateForPDB, null, ap);
+ sview = new AppJmol(pdb, seqsForPdb, null, ap);
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+ sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
}
else
{
return sview;
}
- public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
- SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
- {
- return viewStructures(getViewerType(), ap, pdb, sequenceIs);
- }
-
/**
* Create a new panel controlling a structure viewer.
*
*/
public JalviewStructureDisplayI createView(ViewerType type,
String[] pdbf, String[] id, SequenceI[][] sq,
- AlignmentPanel alignPanel, StructureViewerModel viewerData, String fileloc,
- Rectangle rect, String vid)
+ AlignmentPanel alignPanel, StructureViewerModel viewerData,
+ String fileloc, Rectangle rect, String vid)
{
final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();