import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
*
* @param structureSelectionManager
*/
- public StructureViewer(StructureSelectionManager structureSelectionManager)
+ public StructureViewer(
+ StructureSelectionManager structureSelectionManager)
{
ssm = structureSelectionManager;
}
return sv;
}
-
@Override
public String toString()
{
}
return "New View";
}
+
/**
*
- * @return ViewerType for currently configured structure viewer
+ * @return ViewerType for currently configured structure viewer
*/
public static ViewerType getViewerType()
{
public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
SequenceI[] seqs, AlignmentPanel ap)
{
+ return viewStructures(pdbs, seqs, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
+ {
JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
if (viewer != null)
{
return viewer;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
seqs);
- PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
- new PDBEntry[seqsForPdbs.size()]);
- SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
- new SequenceI[seqsForPdbs.size()][]);
+ PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
+ .toArray(new PDBEntry[seqsForPdbs.size()]);
+ SequenceI[][] theSeqs = seqsForPdbs.values()
+ .toArray(new SequenceI[seqsForPdbs.size()][]);
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
+ return viewStructures(pdb, seqsForPdb, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+ SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
+ {
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
sview.raiseViewer();
return sview;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
- Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return viewer;
}
-
public boolean isBusy()
{
if (sview != null)