*/
package jalview.gui;
+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;
+
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;
import jalview.structure.StructureSelectionManager;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.List;
-
/**
- * 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;
+ /**
+ * decide if new structures are aligned to existing ones
+ */
+ private boolean superposeAdded = true;
+
public enum ViewerType
{
- JMOL, CHIMERA
+ JMOL, CHIMERA, CHIMERAX, PYMOL
};
- public ViewerType getViewerType()
+ /**
+ * Constructor
+ *
+ * @param structureSelectionManager
+ */
+ public StructureViewer(StructureSelectionManager structureSelectionManager)
+ {
+ ssm = structureSelectionManager;
+ }
+
+ /**
+ * Factory to create a proxy for modifying existing structure viewer
+ *
+ */
+ public static StructureViewer reconfigure(
+ JalviewStructureDisplayI display)
+ {
+ StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
+ sv.sview = display;
+ return sv;
+ }
+
+
+ @Override
+ public String toString()
+ {
+ if (sview != null)
+ {
+ return sview.toString();
+ }
+ return "New View";
+ }
+ /**
+ *
+ * @return ViewerType for currently configured structure viewer
+ */
+ public static ViewerType getViewerType()
{
String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
ViewerType.JMOL.name());
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()][]);
+ if (sview != null)
+ {
+ sview.setAlignAddedStructures(superposeAdded);
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+
+ for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
+ {
+ PDBEntry pdb = pdbsForFile[pdbep];
+ if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
+ pdb.getId()))
+ {
+ sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
+ pdb.getId());
+ }
+ }
+
+ sview.updateTitleAndMenus();
+ }
+ }).start();
+ return sview;
+ }
+
+ if (viewerType.equals(ViewerType.JMOL))
+ {
+ sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
+ }
+ else if (viewerType.equals(ViewerType.CHIMERA))
+ {
+ sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+ ap);
+ }
+ else if (viewerType.equals(ViewerType.CHIMERAX))
+ {
+ sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
+ ap);
+ }
+ else if (viewerType.equals(ViewerType.PYMOL))
+ {
+ sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
+ }
+ else
+ {
+ Console.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>();
+ List<SequenceI> seqs = new ArrayList<>();
if (pdbs == null || pdbs.length == 0)
{
return null;
{
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);
}
+ JalviewStructureDisplayI sview = null;
+
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))
+ if (sview != null)
{
- 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());
+ sview.setAlignAddedStructures(superposeAdded);
+ String pdbId = pdb.getId();
+ if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
+ {
+ sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
+ }
+ sview.updateTitleAndMenus();
+ sview.raiseViewer();
+ return sview;
}
- return sview;
- }
-
- protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
- {
- JalviewStructureDisplayI sview = null;
+ ViewerType viewerType = getViewerType();
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
{
sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
}
+ else if (viewerType.equals(ViewerType.CHIMERAX))
+ {
+ sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
+ }
+ else if (viewerType.equals(ViewerType.PYMOL))
+ {
+ sview = new PymolViewer(pdb, seqsForPdb, null, ap);
+ }
else
{
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
/**
- * Create a new panel controlling a structure viewer.
+ * Creates a new panel controlling a structure viewer
*
* @param type
- * @param pdbf
- * @param id
- * @param sq
* @param alignPanel
* @param viewerData
- * @param fileloc
- * @param rect
+ * @param sessionFile
* @param vid
* @return
*/
- public JalviewStructureDisplayI createView(ViewerType type,
- String[] pdbf, String[] id, SequenceI[][] sq,
+ public static JalviewStructureDisplayI createView(ViewerType type,
AlignmentPanel alignPanel, StructureViewerModel viewerData,
- String fileloc, Rectangle rect, String vid)
+ String sessionFile, String vid)
{
- final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
- final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
- final boolean viewerColouring = viewerData.isColourByViewer();
-
- JalviewStructureDisplayI sview = null;
+ JalviewStructureDisplayI viewer = null;
switch (type)
{
case JMOL:
- sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
- useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
+ viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
+ // todo or construct and then openSession(sessionFile)?
break;
case CHIMERA:
- Cache.log.error("Unsupported structure viewer type "
- + type.toString());
+ viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
+ vid);
+ break;
+ case CHIMERAX:
+ viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
+ vid);
+ break;
+ case PYMOL:
+ viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
- Cache.log.error("Unknown structure viewer type " + type.toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
- return sview;
+ return viewer;
+ }
+
+
+ public boolean isBusy()
+ {
+ if (sview != null)
+ {
+ if (!sview.hasMapping())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @param pDBid
+ * @return true if view is already showing PDBid
+ */
+ public boolean hasPdbId(String pDBid)
+ {
+ if (sview == null)
+ {
+ return false;
+ }
+
+ return sview.getBinding().hasPdbId(pDBid);
+ }
+
+ public boolean isVisible()
+ {
+ return sview != null && sview.isVisible();
+ }
+
+ public void setSuperpose(boolean alignAddedStructures)
+ {
+ superposeAdded = alignAddedStructures;
}
}
git://source.jalview.org / jalview.git / blobdiff