/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*/
package jalview.gui;
-import java.awt.Rectangle;
-
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.Viewer;
+import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
+
+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
{
+
+ static
+ {
+ Platform.ensureJmol();
+ }
+
+ private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
+
StructureSelectionManager ssm;
- public enum Viewer
+ /**
+ * decide if new structures are aligned to existing ones
+ */
+ private boolean superposeAdded = true;
+
+ public enum ViewerType
{
JMOL, CHIMERA
- };
+ }
- public Viewer getViewerType()
+ /**
+ * Constructor
+ *
+ * @param structureSelectionManager
+ */
+ public StructureViewer(StructureSelectionManager structureSelectionManager)
{
- String viewType = Cache.getDefault("STRUCTURE_DISPLAY", "JMOL");
- return Viewer.valueOf(viewType);
+ ssm = structureSelectionManager;
}
- public void setViewerType(Viewer type)
+ /**
+ * Factory to create a proxy for modifying existing structure viewer
+ *
+ */
+ public static StructureViewer reconfigure(
+ JalviewStructureDisplayI display)
{
- Cache.setProperty("STRUCTURE_DISPLAY", type.toString());
+ StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
+ sv.sview = display;
+ return sv;
}
- public StructureViewer(StructureSelectionManager structureSelectionManager)
+ @Override
+ public String toString()
{
- ssm = structureSelectionManager;
+ if (sview != null)
+ {
+ return sview.toString();
+ }
+ return "New View";
+ }
+ public ViewerType getViewerType()
+ {
+ String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name());
+ return ViewerType.valueOf(viewType);
}
- public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
- PDBEntry[] pr, SequenceI[][] collateForPDB)
+ public void setViewerType(ViewerType type)
{
- return viewStructures(getViewerType(), ap, pr, collateForPDB);
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
}
- public JalviewStructureDisplayI viewStructures(Viewer viewerType,
- AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+ /**
+ * View multiple PDB entries, each with associated sequences
+ *
+ * @param pdbs
+ * @param seqs
+ * @param ap
+ * @return
+ */
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[] seqs, AlignmentPanel ap)
{
- JalviewStructureDisplayI sview = null;
- if (viewerType.equals(Viewer.JMOL))
+ JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
+ if (viewer != null)
{
- sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ /*
+ * user added structure to an existing viewer - all done
+ */
+ return viewer;
}
- else if (viewerType.equals(Viewer.CHIMERA))
+
+ 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 = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+ 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
{
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
- public JalviewStructureDisplayI viewStructures(Viewer viewerType,
- AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+ /**
+ * 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)
{
- JalviewStructureDisplayI sview = null;
- if (viewerType.equals(Viewer.JMOL))
+ if (pdbs == null || seqs == null || pdbs.length != seqs.length)
{
- sview = new AppJmol(pr, collateForPDB, null, ap);
+ return null;
}
- else if (viewerType.equals(Viewer.CHIMERA))
+
+ /*
+ * 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++)
{
- sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+ 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);
+ }
}
- else
+
+ /*
+ * convert to Map<PDBEntry, SequenceI[]>
+ */
+ Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
+ for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
{
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ List<SequenceI> theSeqs = entry.getValue();
+ result.put(entry.getKey(),
+ theSeqs.toArray(new SequenceI[theSeqs.size()]));
}
- return sview;
+
+ return result;
}
+ /**
+ * 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<>();
+ 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 pdbseq = seqsForPdbs[i++];
+ if (pdbseq != null)
+ {
+ seqs.add(pdbseq);
+ }
+ }
+ return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
+ ap);
+ }
+
+ JalviewStructureDisplayI sview = null;
+
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
- SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
+ SequenceI[] seqsForPdb, AlignmentPanel ap)
{
- return viewStructures(getViewerType(), ap, pdb, sequenceIs);
+ if (sview != null)
+ {
+ 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;
+ }
+ ViewerType viewerType = getViewerType();
+ if (viewerType.equals(ViewerType.JMOL))
+ {
+ sview = new AppJmol(pdb, seqsForPdb, null, ap);
+ }
+ else if (viewerType.equals(ViewerType.CHIMERA))
+ {
+ sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
+ }
+ else
+ {
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ }
+ return sview;
}
- public JalviewStructureDisplayI createView(Viewer jmol, String[] pdbf,
+ /**
+ * Create a new panel controlling a structure viewer.
+ *
+ * @param type
+ * @param pdbf
+ * @param id
+ * @param sq
+ * @param alignPanel
+ * @param viewerData
+ * @param fileloc
+ * @param rect
+ * @param vid
+ * @return
+ */
+ public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
- boolean useinJmolsuperpos, boolean usetoColourbyseq,
- boolean jmolColouring, String fileloc, Rectangle rect, String vid)
+ StructureViewerModel viewerData, String fileloc, Rectangle rect,
+ String vid)
{
- JalviewStructureDisplayI sview = null;
- switch (getViewerType())
+ final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
+ final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
+ final boolean viewerColouring = viewerData.isColourByViewer();
+
+ switch (type)
{
case JMOL:
-
- sview = new AppJmol(pdbf, id, sq, alignPanel, useinJmolsuperpos,
- usetoColourbyseq, jmolColouring, fileloc, rect, vid);
-
+ sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
+ useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
break;
case CHIMERA:
+ Cache.log.error(
+ "Unsupported structure viewer type " + type.toString());
break;
default:
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return sview;
}
+ 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;
+ }
+
+ /**
+ * Launch a minimal implementation of a StructureViewer.
+ *
+ * @param alignPanel
+ * @param pdb
+ * @param seqs
+ * @return
+ */
+ public static StructureViewer launchStructureViewer(
+ AlignmentPanel alignPanel, PDBEntry pdb, SequenceI[] seqs)
+ {
+ return launchStructureViewer(alignPanel, new PDBEntry[] { pdb }, seqs,
+ false, null, null);
+ }
+
+ /**
+ * Launch a structure viewer with or without an open StructureChooser.
+ *
+ * Moved from StructureChooser to enable JalviewJS startup with structure
+ * display.
+ *
+ * @param ap
+ * @param pdbEntriesToView
+ * @param sequences
+ * @param superimpose
+ * @param theViewer
+ * @param pb
+ * @return
+ */
+ protected static StructureViewer launchStructureViewer(
+ final AlignmentPanel ap,
+ final PDBEntry[] pdbEntriesToView, SequenceI[] sequences,
+ boolean superimpose, StructureViewer theViewer,
+ IProgressIndicator pb)
+ {
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ long progressId = sequences.hashCode();
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
+ }
+ if (theViewer == null)
+ {
+ theViewer = new StructureViewer(ssm);
+ }
+ theViewer.setSuperpose(superimpose);
+
+ if (pb != null)
+ {
+ pb.setProgressBar(null, progressId);
+ }
+ if (SiftsSettings.isMapWithSifts())
+ {
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+ for (SequenceI seq : sequences)
+ {
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
+ {
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (seq.getPrimaryDBRefs().isEmpty())
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y), progressId);
+ }
+ SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ if (pb != null)
+ {
+ pb.setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
+ }
+ if (pdbEntriesToView.length > 1)
+ {
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ }
+ theViewer.viewStructures(pdbEntriesToView, sequences, ap);
+ }
+ else
+ {
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ }
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+ }
+ if (pb != null)
+ {
+ pb.setProgressBar(null, progressId);
+ }
+ // remember the last viewer we used...
+ Desktop.getInstance().lastTargetedView = theViewer;
+ return theViewer;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff