X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=7c386f1a8cf63bd953e20adcaa2d22f2b871ae83;hb=bf97c293ad31f6ed5006a97d3a7d079c032652e8;hp=9c9cd1d54cafb7059196178dcb538f8cebbeb9fe;hpb=3ab582bfeeab1563bedf60e97994e63e672d2e31;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 9c9cd1d..7c386f1 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -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; /** @@ -62,9 +62,11 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser implements - IProgressIndicator +public class StructureChooser extends GStructureChooser + implements IProgressIndicator { + private static int MAX_QLENGTH = 7820; + private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -115,9 +117,8 @@ public class StructureChooser extends GStructureChooser implements .getString("status.loading_cached_pdb_entries"), startTime); loadLocalCachedPDBEntries(); updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager - .getString("status.searching_for_pdb_structures"), - startTime); + updateProgressIndicator(MessageManager.getString( + "status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); // revise filter options if no results were found populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); @@ -156,8 +157,8 @@ public class StructureChooser extends GStructureChooser implements Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { FTSRestRequest pdbRequest = new FTSRestRequest(); @@ -195,9 +196,8 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -214,16 +214,16 @@ 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); } } } public void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -257,18 +257,18 @@ public class StructureChooser extends GStructureChooser implements boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - Set 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(entry.getId().toLowerCase()).append(" OR "); + queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) + .append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); } } } @@ -277,7 +277,8 @@ 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)) { @@ -400,8 +401,8 @@ public class StructureChooser extends GStructureChooser implements lbl_loading.setVisible(true); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { @@ -452,12 +453,11 @@ public class StructureChooser extends GStructureChooser implements if (!filteredResponse.isEmpty()) { final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); + Collection reorderedStructuresSet = new LinkedHashSet<>(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - reorderedStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); @@ -481,11 +481,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( - null, - errorMsg.toString(), + JvOptionPane.showMessageDialog(null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -506,9 +504,9 @@ public class StructureChooser extends GStructureChooser implements jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", - selectedSequence.getDisplayId(false))); + chooser.setDialogTitle( + MessageManager.formatMessage("label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( "label.load_pdb_file_associate_with_sequence", selectedSequence.getDisplayId(false))); @@ -538,26 +536,26 @@ public class StructureChooser extends GStructureChooser implements 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)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB); - cmb_filterOption.addItem(cachedOption); - - if (/*!haveData &&*/cachedPDBExists) + cmb_filterOption.addItem( + new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false)); + cmb_filterOption.addItem( + new FilterOption("From File", "-", VIEWS_FROM_FILE, false)); + + if (cachedPDBExists) { + FilterOption cachedOption = new FilterOption("Cached Structures", + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); } @@ -639,22 +637,20 @@ public class StructureChooser extends GStructureChooser implements lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager - .formatMessage("info.no_pdb_entry_found_for", - txt_search.getText()))); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) { lbl_pdbManualFetchStatus.setIcon(warningImage); - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, errorWarning.toString())); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); } - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) { txt_search.setEnabled(true); if (isValidPBDEntry) @@ -679,9 +675,8 @@ public class StructureChooser extends GStructureChooser implements AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) @@ -730,11 +725,10 @@ public class StructureChooser extends GStructureChooser implements @Override public void ok_ActionPerformed() { - final long progressSessionId = System.currentTimeMillis(); final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); - ssm.setProgressIndicator(this); - ssm.setProgressSessionId(progressSessionId); + new Thread(new Runnable() { @Override @@ -752,11 +746,11 @@ 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, - pdbIdColIndex).toString(); + String pdbIdStr = getResultTable() + .getValueAt(row, pdbIdColIndex).toString(); SequenceI selectedSeq = (SequenceI) getResultTable() .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); @@ -766,6 +760,7 @@ public class StructureChooser extends GStructureChooser implements pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } + if (pdbEntry == null) { pdbEntry = new PDBEntry(); @@ -788,14 +783,14 @@ 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, pdbIdColIndex); pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( - row, refSeqColIndex); + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); } SequenceI[] selectedSeqs = selectedSeqsToView @@ -810,7 +805,6 @@ public class StructureChooser extends GStructureChooser implements { selectedSequence = userSelectedSeq; } - String pdbIdStr = txt_search.getText(); PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -831,7 +825,8 @@ public class StructureChooser extends GStructureChooser implements PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] { selectedSequence }); + new SequenceI[] + { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -843,13 +838,15 @@ public class StructureChooser extends GStructureChooser implements } PDBEntry fileEntry = new AssociatePdbFileWithSeq() .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); + new SequenceI[] + { selectedSequence }); } closeAction(preferredHeight); + mainFrame.dispose(); } }).start(); } @@ -873,13 +870,15 @@ public class StructureChooser extends GStructureChooser implements final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer")); + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); final StructureViewer sViewer = new StructureViewer(ssm); + setProgressBar(null, progressId); if (SiftsSettings.isMapWithSifts()) { - List 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 @@ -910,41 +909,37 @@ public class StructureChooser extends GStructureChooser implements if (!seqsWithoutSourceDBRef.isEmpty()) { int y = seqsWithoutSourceDBRef.size(); - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", - y)); + y), progressId); SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; int x = 0; for (SequenceI fSeq : seqsWithoutSourceDBRef) { seqWithoutSrcDBRef[x++] = fSeq; } + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n } } 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, alignPanel); + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); + pdbEntriesToView[0].getId()),progressId); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } + setProgressBar(null, progressId); } /** @@ -953,11 +948,12 @@ public class StructureChooser extends GStructureChooser implements */ @Override public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) { cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -1002,7 +998,7 @@ public class StructureChooser extends GStructureChooser implements String searchTerm = txt_search.getText().toLowerCase(); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList(); + List wantedFields = new ArrayList<>(); FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); @@ -1046,8 +1042,9 @@ public class StructureChooser extends GStructureChooser implements public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); @@ -1056,13 +1053,14 @@ public class StructureChooser extends GStructureChooser implements public class PDBEntryTableModel extends AbstractTableModel { - String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; private List pdbEntries; public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1103,8 +1101,8 @@ public class StructureChooser extends GStructureChooser implements value = entry.getPdbEntry(); break; case 2: - value = entry.getPdbEntry().getChainCode() == null ? "_" : entry - .getPdbEntry().getChainCode(); + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); break; case 3: value = entry.getPdbEntry().getType();