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.sifts.SiftsSettings;
import java.awt.Rectangle;
import java.util.ArrayList;
*/
public class StructureViewer
{
+
+ static
+ {
+ Platform.ensureJmol();
+ }
+
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
- };
+ }
/**
* Constructor
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";
+ }
public ViewerType getViewerType()
{
String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
new PDBEntry[seqsForPdbs.size()]);
SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
new SequenceI[seqsForPdbs.size()][]);
- JalviewStructureDisplayI sview = null;
+ 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, pdbsForFile, theSeqs);
+ sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+ sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+ ap);
}
else
{
private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
SequenceI[] seqsForPdbs, AlignmentPanel ap)
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
if (pdbs == null || pdbs.length == 0)
{
return null;
ap);
}
+ JalviewStructureDisplayI sview = null;
+
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
+ 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();
- JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
final boolean viewerColouring = viewerData.isColourByViewer();
- JalviewStructureDisplayI sview = null;
switch (type)
{
case JMOL:
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