*/
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.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+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;
/**
* A proxy for handling structure viewers, that orchestrates adding selected
*/
public class StructureViewer
{
+
+ static
+ {
+ Platform.loadStaticResource("core/core_jvjmol.z.js",
+ "org.jmol.viewer.Viewer");
+ }
+
+
+
+
private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
StructureSelectionManager ssm;
public enum ViewerType
{
- JMOL, CHIMERA
+ JMOL, CHIMERA, CHIMERAX, PYMOL
};
/**
*
* @param structureSelectionManager
*/
- public StructureViewer(StructureSelectionManager structureSelectionManager)
+ public StructureViewer(
+ StructureSelectionManager structureSelectionManager)
{
ssm = structureSelectionManager;
}
}
return "New View";
}
- public ViewerType getViewerType()
+
+ /**
+ *
+ * @return ViewerType for currently configured structure viewer
+ */
+ public static ViewerType getViewerType()
{
String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
ViewerType.JMOL.name());
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);
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
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
{
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_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 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, AlignmentPanel alignPanel,
- StructureViewerModel viewerData, String fileloc, Rectangle rect,
- String vid)
+ public static JalviewStructureDisplayI createView(ViewerType type,
+ AlignmentPanel alignPanel, StructureViewerModel viewerData,
+ String sessionFile, String vid)
{
- final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
- final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
- final boolean viewerColouring = viewerData.isColourByViewer();
+ 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_VIEWER_TYPE + type.toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
- return sview;
+ return viewer;
}
public boolean isBusy()
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);
+ }
+
+ /**
+ * Adds PDB structures to a new or existing structure viewer
+ *
+ * @param ssm
+ * @param pdbEntriesToView
+ * @param alignPanel
+ * @param sequences
+ * @return
+ */
+ protected static StructureViewer launchStructureViewer(
+ final AlignmentPanel ap, final PDBEntry[] pdbEntriesToView,
+ SequenceI[] sequences, boolean superimpose,
+ StructureViewer theViewer, IProgressIndicator pb)
+ {
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ if (theViewer == null)
+ theViewer = new StructureViewer(ssm);
+ long progressId = sequences.hashCode();
+ if (pb != null)
+ pb.setProgressBar(MessageManager.getString(
+ "status.launching_3d_structure_viewer"), progressId);
+ theViewer.setSuperpose(superimpose);
+
+ /*
+ * remember user's choice of superimpose or not
+ */
+ Cache.setProperty(StructureChooser.AUTOSUPERIMPOSE,
+ Boolean.valueOf(superimpose).toString());
+
+ 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...
+ StructureChooser.lastTargetedView = theViewer;
+ return theViewer;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff