import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
{
private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- private static final int MAX_QLENGTH = 7820;
+ private static int MAX_QLENGTH = 7820;
- protected SequenceI selectedSequence;
+ private SequenceI selectedSequence;
- public SequenceI[] selectedSequences;
+ private SequenceI[] selectedSequences;
private IProgressIndicator progressIndicator;
- protected Collection<FTSData> discoveredStructuresSet;
+ private Collection<FTSData> discoveredStructuresSet;
- protected FTSRestRequest lastPdbRequest;
+ private FTSRestRequest lastPdbRequest;
- protected FTSRestClientI pdbRestClient;
+ private FTSRestClientI pdbRestClient;
- protected String selectedPdbFileName;
+ private String selectedPdbFileName;
- protected boolean isValidPBDEntry;
+ private boolean isValidPBDEntry;
- protected boolean cachedPDBExists;
+ private boolean cachedPDBExists;
+
+ private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
* structures may be added. If this list is empty then it, and the 'Add'
* button, are hidden.
*/
- protected void discoverStructureViews()
+ private void discoverStructureViews()
{
- Desktop desktop = Desktop.getInstance();
- if (desktop != null)
+ if (Desktop.instance != null)
{
targetView.removeAllItems();
- if (desktop.lastTargetedView != null
- && !desktop.lastTargetedView.isVisible())
+ if (lastTargetedView != null && !lastTargetedView.isVisible())
{
- desktop.lastTargetedView = null;
+ lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : desktop
+ for (StructureViewerBase view : Desktop.instance
.getStructureViewers(null, null))
{
- StructureViewer viewHandler = (desktop.lastTargetedView != null
- && desktop.lastTargetedView.sview == view)
- ? desktop.lastTargetedView
+ StructureViewer viewHandler = (lastTargetedView != null
+ && lastTargetedView.sview == view) ? lastTargetedView
: StructureViewer.reconfigure(view);
if (view.isLinkedWith(ap))
if (targetView.getItemCount() > 0)
{
targetView.setVisible(true);
- if (desktop.lastTargetedView != null)
+ if (lastTargetedView != null)
{
- targetView.setSelectedItem(desktop.lastTargetedView);
+ targetView.setSelectedItem(lastTargetedView);
}
else
{
/**
* structure viewer opened by this dialog, or null
*/
- protected StructureViewer sViewer = null;
+ private StructureViewer sViewer = null;
public void showStructures(boolean waitUntilFinished)
{
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
final int preferredHeight = pnl_filter.getHeight();
Runnable viewStruc = new Runnable()
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[]
{ selectedSequence });
}
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = AssociatePdbFileWithSeq
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true);
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
sViewer = launchStructureViewer(
- ap, new PDBEntry[]
- { fileEntry },
+ ssm, new PDBEntry[]
+ { fileEntry }, ap,
new SequenceI[]
{ selectedSequence });
}
}
}
- protected PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
Objects.requireNonNull(pdbEntries);
* Answers a structure viewer (new or existing) configured to superimpose
* added structures or not according to the user's choice
*
+ * @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer()
+ StructureViewer getTargetedStructureViewer(
+ StructureSelectionManager ssm)
{
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
- Object sv = (targetView == null ? null : targetView.getSelectedItem());
+ Object sv = targetView.getSelectedItem();
return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
}
/**
* Adds PDB structures to a new or existing structure viewer
*
- * @param ap
+ * @param ssm
* @param pdbEntriesToView
+ * @param alignPanel
* @param sequences
- * @param superimpose
- * @return viewer
+ * @return
*/
- protected StructureViewer launchStructureViewer(
- AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
- SequenceI[] selectedSeqs)
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm,
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
{
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
+ final StructureViewer theViewer = getTargetedStructureViewer(ssm);
boolean superimpose = chk_superpose.isSelected();
+ theViewer.setSuperpose(superimpose);
+
/*
* remember user's choice of superimpose or not
*/
Cache.setProperty(AUTOSUPERIMPOSE,
Boolean.valueOf(superimpose).toString());
- return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
- superimpose, getTargetedStructureViewer(), progressBar);
+
+ 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();
+ 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);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
+ if (pdbEntriesToView.length > 1)
+ {
+ setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ }
+ else
+ {
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
+ setProgressBar(null, progressId);
+ // remember the last viewer we used...
+ lastTargetedView = theViewer;
+ return theViewer;
}
/**
protected void txt_search_ActionPerformed()
{
String text = txt_search.getText().trim();
- if (text.length() >= PDB_ID_MIN)
- {
+ if (text.length() >= PDB_ID_MIN)
new Thread()
{
}
}.start();
}
- }
@Override
protected void tabRefresh()
@Override
public void setProgressBar(String message, long id)
{
- if (progressBar != null)
- {
- progressBar.setProgressBar(message, id);
- }
+ progressBar.setProgressBar(message, id);
}
@Override
git://source.jalview.org / jalview.git / blobdiff