X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=bff6d6f5e69a94b28a902c82d6e9d1408d89c900;hb=d980f203d66517042c7d2707ec300c653cae1892;hp=8dbe0c250e041edd7f12dbf426e6599b176ae4fa;hpb=80edaa84d6d9beac9f0d2c71b50b7b56fd393427;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 8dbe0c2..bff6d6f 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -32,10 +32,14 @@ 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.phyre2.Phyre2Client; +import jalview.ws.phyre2.Phyre2SummaryPojo; import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; @@ -45,12 +49,12 @@ import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; import java.util.Objects; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; -import javax.swing.JOptionPane; import javax.swing.table.AbstractTableModel; /** @@ -63,7 +67,7 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private boolean structuresDiscovered = false; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -77,10 +81,12 @@ public class StructureChooser extends GStructureChooser implements private FTSRestClientI pdbRestCleint; - private String selectedPdbFileName; + private String selectedStructureFileName; private boolean isValidPBDEntry; + private boolean cachedPDBExists; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -101,6 +107,8 @@ public class StructureChooser extends GStructureChooser implements progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + // ensure a filter option is in force for search + populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -115,7 +123,8 @@ public class StructureChooser extends GStructureChooser implements .getString("status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); - populateFilterComboBox(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -159,6 +168,10 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(500); pdbRequest.setFieldToSearchBy("("); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), + !chk_invertFilter.isSelected()); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); @@ -187,9 +200,8 @@ public class StructureChooser extends GStructureChooser implements && !discoveredStructuresSet.isEmpty()) { getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; + JvSummaryTable.getTableModel(lastPdbRequest, + discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -206,9 +218,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), + JvOptionPane.showMessageDialog(this, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -231,7 +243,7 @@ public class StructureChooser extends GStructureChooser implements } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -249,20 +261,18 @@ public class StructureChooser extends GStructureChooser implements boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - HashSet seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet(); - if (seq.getAllPDBEntries() != null) + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) { for (PDBEntry entry : seq.getAllPDBEntries()) { if (isValidSeqName(entry.getId())) { - queryBuilder.append("pdb_id") - .append(":") -.append(entry.getId().toLowerCase()) - .append(" OR "); + queryBuilder.append("pdb_id:") + .append(entry.getId().toLowerCase()).append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); } } } @@ -271,26 +281,22 @@ public class StructureChooser extends GStructureChooser implements { for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { - queryBuilder -.append("uniprot_accession").append(":") - .append(getDBRefId(dbRef)) - .append(" OR "); - queryBuilder -.append("uniprot_id") - .append(":") + queryBuilder.append("uniprot_accession:") .append(getDBRefId(dbRef)).append(" OR "); + queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) + .append(" OR "); isUniProtRefsFound = true; } else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append("pdb_id") - .append(":").append(getDBRefId(dbRef).toLowerCase()) - .append(" OR "); + queryBuilder.append("pdb_id:") + .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); isPDBRefsFound = true; } else @@ -345,7 +351,6 @@ public class StructureChooser extends GStructureChooser implements .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); } - /** * Ensures sequence ref names are not less than 3 characters and does not * contain a database name @@ -456,11 +461,11 @@ public class StructureChooser extends GStructureChooser implements reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); getResultTable().setModel( - FTSRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); + JvSummaryTable.getTableModel(lastPdbRequest, + reorderedStructuresSet)); - FTSRestResponse.configureTableColumn(getResultTable(), - wantedFields); + JvSummaryTable.configureTableColumn(getResultTable(), + wantedFields, tempUserPrefs); getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); getResultTable().getColumn("Ref Sequence").setMinWidth(100); getResultTable().getColumn("Ref Sequence").setMaxWidth(200); @@ -481,11 +486,11 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( + JvOptionPane.showMessageDialog( null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -516,8 +521,8 @@ public class StructureChooser extends GStructureChooser implements int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + selectedStructureFileName = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedStructureFileName); validateSelections(); } } @@ -526,34 +531,50 @@ public class StructureChooser extends GStructureChooser implements * Populates the filter combo-box options dynamically depending on discovered * structures */ - @Override - protected void populateFilterComboBox() + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExists) { - if (isStructuresDiscovered()) + /* + * temporarily suspend the change listener behaviour + */ + cmb_filterOption.removeItemListener(this); + + cmb_filterOption.removeAllItems(); + if (haveData) { cmb_filterOption.addItem(new FilterOption("Best Quality", - "overall_quality", VIEWS_FILTER)); + "overall_quality", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Best Resolution", - "resolution", VIEWS_FILTER)); + "resolution", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - "number_of_protein_chains", VIEWS_FILTER)); + "number_of_protein_chains", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - "number_of_bound_molecules", VIEWS_FILTER)); + "number_of_bound_molecules", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - "number_of_polymer_residues", VIEWS_FILTER)); + "number_of_polymer_residues", VIEWS_FILTER, true)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); + VIEWS_ENTER_ID, false)); cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + VIEWS_FROM_FILE, false)); + + if (cachedPDBExists) + { + FilterOption cachedOption = new FilterOption("Cached PDB Entries", + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); + cmb_filterOption.setSelectedItem(cachedOption); + } + + cmb_filterOption.addItem(new FilterOption( + "Predict 3D Model with Phyre2", "-", VIEWS_PHYRE2_PREDICTION, + false)); + cmb_filterOption.addItemListener(this); } /** * Updates the displayed view based on the selected filter option */ - @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -569,6 +590,12 @@ public class StructureChooser extends GStructureChooser implements chk_invertFilter.setVisible(true); filterResultSet(selectedFilterOpt.getValue()); } + else if (selectedFilterOpt.getView() == VIEWS_PHYRE2_PREDICTION) + { + mainFrame.setTitle(MessageManager + .getString("label.phyre2_model_prediction")); + phyre2InputAssSeqPanel.loadCmbAssSeq(); + } else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { @@ -613,6 +640,14 @@ public class StructureChooser extends GStructureChooser implements { validateAssociationFromFile(); } + else if (currentView == VIEWS_PHYRE2_PREDICTION) + { + validateAssociationFromPhyre2(); + if (getPhyreResultTable().getSelectedRows().length > 0) + { + btn_view.setEnabled(true); + } + } } /** @@ -671,7 +706,7 @@ public class StructureChooser extends GStructureChooser implements "-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); - if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) + if (selectedStructureFileName != null && selectedStructureFileName.length() > 0) { btn_view.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); @@ -684,6 +719,25 @@ public class StructureChooser extends GStructureChooser implements } } + /** + * Validates inputs for Phyre2 3D Model prediction + */ + public void validateAssociationFromPhyre2() + { + AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) phyre2InputAssSeqPanel + .getCmb_assSeq().getSelectedItem(); + if (selectedSequences.length == 1 + || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( + "-Select Associated Seq-"))) + { + btn_runPhyre2Prediction.setEnabled(true); + } + else + { + btn_runPhyre2Prediction.setEnabled(false); + } + } + @Override public void cmbAssSeqStateChanged() { @@ -718,101 +772,104 @@ public class StructureChooser extends GStructureChooser implements public void ok_ActionPerformed() { final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); + ssm.setMappingForPhyre2Model(false); new Thread(new Runnable() { @Override public void run() { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) - { + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER) + { int pdbIdColIndex = getResultTable().getColumn("PDB Id") .getModelIndex(); int refSeqColIndex = getResultTable().getColumn("Ref Sequence") - .getModelIndex(); + .getModelIndex(); int[] selectedRows = getResultTable().getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + List selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { String pdbIdStr = getResultTable().getValueAt(row, - pdbIdColIndex) - .toString(); + pdbIdColIndex).toString(); SequenceI selectedSeq = (SequenceI) getResultTable() - .getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); if (pdbEntry == null) { pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + } + pdbEntriesToView[count++] = pdbEntry; + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); - } - else if (currentView == VIEWS_LOCAL_PDB) - { - int[] selectedRows = tbl_local_pdb.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; + else if (currentView == VIEWS_LOCAL_PDB) + { + int[] selectedRows = tbl_local_pdb.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") .getModelIndex(); - int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") - .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); - pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + List selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( + row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + } + else if (currentView == VIEWS_ENTER_ID) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } - String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); + + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); if (pdbIdStr.split(":").length > 1) { - pdbEntry.setChainCode(pdbIdStr.split(":")[1]); + pdbEntry.setId(pdbIdStr.split(":")[0]); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); } - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - } + else + { + pdbEntry.setId(pdbIdStr); + } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } - PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } @@ -824,20 +881,99 @@ public class StructureChooser extends GStructureChooser implements { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, + PDBEntry fileEntry = new AssociateStructureFileWithSeq() + .associateStructureWithSeq(selectedStructureFileName, + DataSourceType.FILE, selectedSequence, true, Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence }); - } - mainFrame.dispose(); + } + else if (currentView == VIEWS_PHYRE2_PREDICTION) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) phyre2InputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + int templateColIndex = getPhyreResultTable() + .getColumn("Template") + .getModelIndex(); + int[] selectedRows = getPhyreResultTable().getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + for (int row : selectedRows) + { + String templateId = getPhyreResultTable().getValueAt(row, + templateColIndex).toString(); + String structureFile = phyre2ResultDirectory + templateId + + ".pdb"; + pdbEntriesToView[count++] = new AssociateStructureFileWithSeq() + .associateStructureWithSeq(structureFile, + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); + } + + final StructureSelectionManager ssm = ap + .getStructureSelectionManager(); + ssm.setMappingForPhyre2Model(true); + final long progressSessionId = System.currentTimeMillis(); + ssm.setProgressSessionId(progressSessionId); + + SequenceI[] sequences = new SequenceI[] { selectedSequence }; + + ssm.setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer")); + final StructureViewer sViewer = new StructureViewer(ssm); + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] { seq }); + } + SequenceI[][] collatedSeqs = seqsMap + .toArray(new SequenceI[0][0]); + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager + .getString("status.fetching_3d_structures_for_selected_entries")); + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, ap); + } + else + { + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId())); + sViewer.viewStructures(pdbEntriesToView[0], sequences, ap); + } + } + closeAction(preferredHeight); } }).start(); } + private String phyre2ResultDirectory; + + @Override + public void predict3DModelWithPhyre2() + { + // TODO implement code for submitting sequence to Phyre2 service, and code + // for getting the result directory when the job completes, this is + // currently hard-wired to the directory of result for FER_CAPAN/1-144 + phyre2ResultDirectory = "examples/testdata/phyre2results/56da5616b4559c93/"; + String summaryhtml = phyre2ResultDirectory + "summary.html"; + // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for + // Phyre2 result summary is made available + List phyreResults = Phyre2Client + .parsePhyre2ResultSummaryTable(summaryhtml); + getPhyreResultTable() + .setModel(Phyre2Client.getTableModel(phyreResults)); + Phyre2Client.configurePhyreResultTable(getPhyreResultTable()); + } + private PDBEntry getFindEntry(String id, Vector pdbEntries) { Objects.requireNonNull(id); @@ -865,17 +1001,34 @@ public class StructureChooser extends GStructureChooser implements if (SiftsSettings.isMapWithSifts()) { - // TODO: prompt user if there are lots of sequences without dbrefs. - // It can take a long time if we need to fetch all dbrefs for all - // sequences! - ArrayList seqsWithoutSourceDBRef = new ArrayList(); + List 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) { - if (seq.getSourceDBRef() == null && seq.getDBRefs() == null) + PDBEntry pdbe = pdbEntriesToView[p++]; + if (pdbe != null && pdbe.getFile() != null) { - seqsWithoutSourceDBRef.add(seq); - continue; + StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); + if (smm != null && smm.length > 0) + { + for (StructureMapping sm : smm) + { + if (sm.getSequence() == seq) + { + continue; + } + } } + } + if (seq.getPrimaryDBRefs().size() == 0) + { + seqsWithoutSourceDBRef.add(seq); + continue; + } } if (!seqsWithoutSourceDBRef.isEmpty()) { @@ -946,12 +1099,8 @@ public class StructureChooser extends GStructureChooser implements public boolean isStructuresDiscovered() { - return structuresDiscovered; - } - - public void setStructuresDiscovered(boolean structuresDiscovered) - { - this.structuresDiscovered = structuresDiscovered; + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } public Collection getDiscoveredStructuresSet() @@ -980,8 +1129,7 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("(pdb_id:"); pdbRequest.setWantedFields(wantedFields); - pdbRequest -.setSearchTerm(searchTerm + ")"); + pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); pdbRestCleint = PDBFTSRestClient.getInstance(); wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());