package jalview.gui;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-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;
import java.util.Collection;
import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
+import jalview.jbgui.GStructureChooser;
+import jalview.util.MessageManager;
+
/**
* Provides the behaviors for the Structure chooser Panel
*
public class StructureChooser extends GStructureChooser
implements IProgressIndicator
{
- private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+ static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
private static int MAX_QLENGTH = 7820;
private boolean cachedPDBExists;
- private static StructureViewer lastTargetedView = null;
+ static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
*/
private void discoverStructureViews()
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
targetView.removeAllItems();
if (lastTargetedView != null && !lastTargetedView.isVisible())
lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : Desktop.instance
+ for (StructureViewerBase view : Desktop.getInstance()
.getStructureViewers(null, null))
{
StructureViewer viewHandler = (lastTargetedView != null
if (view.isLinkedWith(ap))
{
- targetView.insertItemAt(viewHandler,
- linkedViewsAt++);
+ targetView.insertItemAt(viewHandler, linkedViewsAt++);
}
else
{
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<>();
+ /*
+ * note PDBs as DBRefEntry so they are not duplicated in query
+ */
+ Set<String> pdbids = new HashSet<>();
+
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
{
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
- .append(" OR ");
+ String id = entry.getId().toLowerCase();
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
+ pdbids.add(id);
}
}
}
{
for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- DBRefEntry dbRef = refs.get(ib);
+ DBRefEntry dbRef = refs.get(ib);
if (isValidSeqName(getDBRefId(dbRef))
&& queryBuilder.length() < MAX_QLENGTH)
{
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id:")
- .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
- isPDBRefsFound = true;
+ String id = getDBRefId(dbRef).toLowerCase();
+ if (!pdbids.contains(id))
+ {
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
}
else
{
@Override
protected void pdbFromFile_actionPerformed()
{
- // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
+ // StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
if (cachedPDBExist)
{
FilterOption cachedOption = new FilterOption(
- MessageManager.getString("label.cached_structures"),
- "-", VIEWS_LOCAL_PDB, false);
+ MessageManager.getString("label.cached_structures"), "-",
+ VIEWS_LOCAL_PDB, false);
cmb_filterOption.addItem(cachedOption);
cmb_filterOption.setSelectedItem(cachedOption);
}
}
return found;
}
-
+
/**
* Handles the 'New View' action
*/
public void showStructures(boolean waitUntilFinished)
{
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
final int preferredHeight = pnl_filter.getHeight();
+ final StructureViewer theViewer = getTargetedStructureViewer();
+ boolean superimpose = chk_superpose.isSelected();
+
Runnable viewStruc = new Runnable()
{
@Override
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = restable.getColumn("PDB Id")
- .getModelIndex();
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
int refSeqColIndex = restable.getColumn("Ref Sequence")
.getModelIndex();
int[] selectedRows = restable.getSelectedRows();
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- String pdbIdStr = restable
- .getValueAt(row, pdbIdColIndex).toString();
- SequenceI selectedSeq = (SequenceI) restable
- .getValueAt(row, refSeqColIndex);
+ String pdbIdStr = restable.getValueAt(row, pdbIdColIndex)
+ .toString();
+ SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+ refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
if (pdbEntry == null)
{
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
+ pdbEntry = new PDBEntry(pdbIdStr, null, "pdb");
selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
}
pdbEntriesToView[count++] = pdbEntry;
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
new SequenceI[]
- { selectedSequence });
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
else if (currentView == VIEWS_FROM_FILE)
{
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
-
- sViewer = launchStructureViewer(
- ssm, new PDBEntry[]
- { fileEntry }, ap,
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
new SequenceI[]
- { selectedSequence });
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
SwingUtilities.invokeLater(new Runnable()
{
* @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer(
- StructureSelectionManager ssm)
- {
- Object sv = targetView.getSelectedItem();
-
- return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
- }
-
- /**
- * Adds PDB structures to a new or existing structure viewer
- *
- * @param ssm
- * @param pdbEntriesToView
- * @param alignPanel
- * @param sequences
- * @return
- */
- private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
+ StructureViewer getTargetedStructureViewer()
{
- 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());
-
- 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;
+ return (StructureViewer) targetView.getSelectedItem();
}
/**
&& !discoveredStructuresSet.isEmpty();
}
- protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
+ // this.
// Doing a search for "1" or "1c" is valuable?
// Those work but are enormously slow.
protected void txt_search_ActionPerformed()
{
String text = txt_search.getText().trim();
- if (text.length() >= PDB_ID_MIN)
- new Thread()
- {
-
- @Override
- public void run()
+ if (text.length() >= PDB_ID_MIN)
+ new Thread()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (text.length() > 0)
+
+ @Override
+ public void run()
{
- String searchTerm = text.toLowerCase();
- searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<>();
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(searchTerm + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestClient = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestClient.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (text.length() > 0)
{
- validateSelections();
- }
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
+ String searchTerm = text.toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(searchTerm + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
}
+ validateSelections();
}
- validateSelections();
- }
- }.start();
+ }.start();
}
@Override
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(long id, IProgressIndicatorHandler handler)
{
return sViewer == null ? null : sViewer.sview;
}
+
}