X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3e516a621b58bc6421027ef62559ccef480f154f;hb=ef39fb4e4ab6c38dd20255f4a60609a6af581dcf;hp=7d8f1bfa1365de768137e4ee8ccf0bf39219fbb2;hpb=33c24a4b371cef971d8728295a24e87fbf6bb5a8;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 7d8f1bf..3e516a6 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -32,6 +32,7 @@ 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; @@ -52,7 +53,6 @@ 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; /** @@ -65,7 +65,7 @@ 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; @@ -83,6 +83,8 @@ public class StructureChooser extends GStructureChooser implements private boolean isValidPBDEntry; + private boolean cachedPDBExists; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -103,6 +105,8 @@ 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 @@ -117,7 +121,8 @@ 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(); @@ -161,6 +166,10 @@ 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); @@ -190,8 +199,7 @@ public class StructureChooser extends GStructureChooser implements { getResultTable().setModel( FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; + discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -208,9 +216,9 @@ 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); } } } @@ -233,7 +241,7 @@ public class StructureChooser extends GStructureChooser implements } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -253,17 +261,16 @@ public class StructureChooser extends GStructureChooser implements StringBuilder queryBuilder = new StringBuilder(); 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(entry.getId().toLowerCase()) - .append(" OR "); + .append(entry.getId().toLowerCase()).append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); } } } @@ -272,13 +279,13 @@ 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(getDBRefId(dbRef)) - .append(" OR "); + .append(getDBRefId(dbRef)).append(" OR "); queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) .append(" OR "); isUniProtRefsFound = true; @@ -287,8 +294,7 @@ public class StructureChooser extends GStructureChooser implements { queryBuilder.append("pdb_id:") - .append(getDBRefId(dbRef).toLowerCase()) - .append(" OR "); + .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); isPDBRefsFound = true; } else @@ -343,7 +349,6 @@ 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 @@ -454,8 +459,8 @@ public class StructureChooser extends GStructureChooser implements reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); getResultTable().setModel( - FTSRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); + FTSRestResponse.getTableModel(lastPdbRequest, + reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); @@ -479,11 +484,11 @@ 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); } } @@ -524,34 +529,47 @@ 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.addItemListener(this); } /** * Updates the displayed view based on the selected filter option */ - @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -737,7 +755,7 @@ public class StructureChooser extends GStructureChooser implements int[] selectedRows = getResultTable().getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { String pdbIdStr = getResultTable().getValueAt(row, @@ -773,7 +791,7 @@ public class StructureChooser extends GStructureChooser implements .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, @@ -817,19 +835,19 @@ public class StructureChooser extends GStructureChooser implements PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, + selectedSequence, true, Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence }); @@ -888,9 +906,9 @@ public class StructureChooser extends GStructureChooser implements } if (seq.getPrimaryDBRefs().size() == 0) { - seqsWithoutSourceDBRef.add(seq); - continue; - } + seqsWithoutSourceDBRef.add(seq); + continue; + } } if (!seqsWithoutSourceDBRef.isEmpty()) { @@ -963,12 +981,8 @@ 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() @@ -997,8 +1011,7 @@ 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());