/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import java.awt.Rectangle;
import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
/**
- * proxy for handling structure viewers.
- *
- * this allows new views to be created with the currently configured viewer, the
- * preferred viewer to be set/read and existing views created previously with a
- * particular viewer to be recovered
+ * A proxy for handling structure viewers, that orchestrates adding selected
+ * structures, associated with sequences in Jalview, to an existing viewer, or
+ * opening a new one. Currently supports either Jmol or Chimera as the structure
+ * viewer.
*
* @author jprocter
*/
public class StructureViewer
{
+ private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
+
StructureSelectionManager ssm;
public enum ViewerType
JMOL, CHIMERA
};
+ /**
+ * Constructor
+ *
+ * @param structureSelectionManager
+ */
+ public StructureViewer(StructureSelectionManager structureSelectionManager)
+ {
+ ssm = structureSelectionManager;
+ }
+
public ViewerType getViewerType()
{
String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
}
- public StructureViewer(StructureSelectionManager structureSelectionManager)
- {
- ssm = structureSelectionManager;
- }
-
/**
* View multiple PDB entries, each with associated sequences
*
* @param pdbs
- * @param seqsForPdbs
+ * @param seqs
* @param ap
* @return
*/
public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
- SequenceI[][] seqsForPdbs, AlignmentPanel ap)
+ SequenceI[] seqs, AlignmentPanel ap)
{
- JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqsForPdbs, ap);
+ JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
if (viewer != null)
{
+ /*
+ * user added structure to an existing viewer - all done
+ */
return viewer;
}
- return viewStructures(getViewerType(), pdbs, seqsForPdbs, ap);
+
+ ViewerType 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()][]);
+ JalviewStructureDisplayI sview = null;
+ if (viewerType.equals(ViewerType.JMOL))
+ {
+ sview = new AppJmol(ap, pdbsForFile, theSeqs);
+ }
+ else if (viewerType.equals(ViewerType.CHIMERA))
+ {
+ sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+ }
+ else
+ {
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ }
+ return sview;
+ }
+
+ /**
+ * Converts the list of selected PDB entries (possibly including duplicates
+ * for multiple chains), and corresponding sequences, into a map of sequences
+ * for each distinct PDB file. Returns null if either argument is null, or
+ * their lengths do not match.
+ *
+ * @param pdbs
+ * @param seqs
+ * @return
+ */
+ Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
+ SequenceI[] seqs)
+ {
+ if (pdbs == null || seqs == null || pdbs.length != seqs.length)
+ {
+ return null;
+ }
+
+ /*
+ * we want only one 'representative' PDBEntry per distinct file name
+ * (there may be entries for distinct chains)
+ */
+ Map<String, PDBEntry> pdbsSeen = new HashMap<>();
+
+ /*
+ * LinkedHashMap preserves order of PDB entries (significant if they
+ * will get superimposed to the first structure)
+ */
+ Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
+ for (int i = 0; i < pdbs.length; i++)
+ {
+ PDBEntry pdb = pdbs[i];
+ SequenceI seq = seqs[i];
+ String pdbFile = pdb.getFile();
+ if (pdbFile == null || pdbFile.length() == 0)
+ {
+ pdbFile = pdb.getId();
+ }
+ if (!pdbsSeen.containsKey(pdbFile))
+ {
+ pdbsSeen.put(pdbFile, pdb);
+ pdbSeqs.put(pdb, new ArrayList<SequenceI>());
+ }
+ else
+ {
+ pdb = pdbsSeen.get(pdbFile);
+ }
+ List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
+ if (!seqsForPdb.contains(seq))
+ {
+ seqsForPdb.add(seq);
+ }
+ }
+
+ /*
+ * convert to Map<PDBEntry, SequenceI[]>
+ */
+ Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
+ for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
+ {
+ List<SequenceI> theSeqs = entry.getValue();
+ result.put(entry.getKey(),
+ theSeqs.toArray(new SequenceI[theSeqs.size()]));
+ }
+
+ return result;
}
/**
* @return
*/
private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
- SequenceI[][] seqsForPdbs, AlignmentPanel ap)
+ SequenceI[] seqsForPdbs, AlignmentPanel ap)
{
List<SequenceI> seqs = new ArrayList<SequenceI>();
if (pdbs == null || pdbs.length == 0)
{
return null;
}
- SequenceI[] pdbseqs = seqsForPdbs[i++];
- if (pdbseqs != null)
+ SequenceI pdbseq = seqsForPdbs[i++];
+ if (pdbseq != null)
{
- for (SequenceI sq : pdbseqs)
- {
- seqs.add(sq);
- }
+ seqs.add(pdbseq);
}
}
- return viewStructures(pdbs[0],
- seqs.toArray(new SequenceI[seqs.size()]), ap);
+ 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, pdbs, ap.av.collateForPDB(pdbs));
- }
- else if (viewerType.equals(ViewerType.CHIMERA))
- {
- sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
- }
- else
- {
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
- }
- return sview;
- }
-
- protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
- {
+ ViewerType viewerType = getViewerType();
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
}
else
{
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
* @param vid
* @return
*/
- public JalviewStructureDisplayI createView(ViewerType type,
- String[] pdbf, String[] id, SequenceI[][] sq,
- AlignmentPanel alignPanel, StructureViewerModel viewerData,
- String fileloc, Rectangle rect, String vid)
+ public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
+ String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
+ StructureViewerModel viewerData, String fileloc, Rectangle rect,
+ String vid)
{
final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
break;
case CHIMERA:
- Cache.log.error("Unsupported structure viewer type "
- + type.toString());
+ Cache.log.error(
+ "Unsupported structure viewer type " + type.toString());
break;
default:
- Cache.log.error("Unknown structure viewer type " + type.toString());
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return sview;
}