+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-
-package jalview.gui;
-
-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.jbgui.GStructureChooser;
-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 java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-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;
-
-/**
- * Provides the behaviors for the Structure chooser Panel
- *
- * @author tcnofoegbu
- *
- */
-@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser implements
- IProgressIndicator
-{
- private boolean structuresDiscovered = false;
-
- private SequenceI selectedSequence;
-
- private SequenceI[] selectedSequences;
-
- private IProgressIndicator progressIndicator;
-
- private Collection<FTSData> discoveredStructuresSet;
-
- private FTSRestRequest lastPdbRequest;
-
- private FTSRestClientI pdbRestCleint;
-
- private String selectedPdbFileName;
-
- private boolean isValidPBDEntry;
-
- public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
- AlignmentPanel ap)
- {
- this.ap = ap;
- this.selectedSequence = selectedSeq;
- this.selectedSequences = selectedSeqs;
- this.progressIndicator = (ap == null) ? null : ap.alignFrame;
- init();
- }
-
- /**
- * Initializes parameters used by the Structure Chooser Panel
- */
- public void init()
- {
- if (!Jalview.isHeadlessMode())
- {
- progressBar = new ProgressBar(this.statusPanel, this.statusBar);
- }
-
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- long startTime = System.currentTimeMillis();
- updateProgressIndicator(MessageManager
- .getString("status.loading_cached_pdb_entries"), startTime);
- loadLocalCachedPDBEntries();
- updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager
- .getString("status.searching_for_pdb_structures"),
- startTime);
- fetchStructuresMetaData();
- populateFilterComboBox();
- updateProgressIndicator(null, startTime);
- mainFrame.setVisible(true);
- updateCurrentView();
- }
- });
- discoverPDBStructuresThread.start();
- }
-
- /**
- * Updates the progress indicator with the specified message
- *
- * @param message
- * displayed message for the operation
- * @param id
- * unique handle for this indicator
- */
- public void updateProgressIndicator(String message, long id)
- {
- if (progressIndicator != null)
- {
- progressIndicator.setProgressBar(message, id);
- }
- }
-
- /**
- * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
- * selection group
- */
- public void fetchStructuresMetaData()
- {
- long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
- .getStructureSummaryFields();
-
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
- for (SequenceI seq : selectedSequences)
- {
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq);
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- e.printStackTrace();
- errors.add(e.getMessage());
- continue;
- }
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- discoveredStructuresSet.addAll(resultList.getSearchSummary());
- }
- }
-
- int noOfStructuresFound = 0;
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- if (discoveredStructuresSet != null
- && !discoveredStructuresSet.isEmpty())
- {
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
- noOfStructuresFound = discoveredStructuresSet.size();
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_no_of_structures",
- noOfStructuresFound, totalTime));
- }
- else
- {
- mainFrame.setTitle(MessageManager
- .getString("label.structure_chooser_manual_association"));
- if (errors.size() > 0)
- {
- StringBuilder errorMsg = new StringBuilder();
- for (String error : errors)
- {
- errorMsg.append(error).append("\n");
- }
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
- MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
- }
-
- public void loadLocalCachedPDBEntries()
- {
- ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
- for (SequenceI seq : selectedSequences)
- {
- if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getAllPDBEntries() != null)
- {
- for (PDBEntry pdbEntry : seq.getDatasetSequence()
- .getAllPDBEntries())
- {
- if (pdbEntry.getFile() != null)
- {
- entries.add(new CachedPDB(seq, pdbEntry));
- }
- }
- }
- }
-
- PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
- tbl_local_pdb.setModel(tableModelx);
- }
-
- /**
- * Builds a query string for a given sequences using its DBRef entries
- *
- * @param seq
- * the sequences to build a query for
- * @return the built query string
- */
-
- public static String buildQuery(SequenceI seq)
- {
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
-
- if (seq.getAllPDBEntries() != null)
- {
- for (PDBEntry entry : seq.getAllPDBEntries())
- {
- if (isValidSeqName(entry.getId()))
- {
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
- .append(" OR ");
- isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
- }
- }
- }
-
- if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
- {
- for (DBRefEntry dbRef : seq.getDBRefs())
- {
- if (isValidSeqName(getDBRefId(dbRef)))
- {
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
- {
- queryBuilder
-.append("uniprot_accession").append(":")
- .append(getDBRefId(dbRef))
- .append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
- .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 ");
- isPDBRefsFound = true;
- }
- else
- {
- seqRefs.add(getDBRefId(dbRef));
- }
- }
- }
- }
-
- if (!isPDBRefsFound && !isUniProtRefsFound)
- {
- String seqName = seq.getName();
- seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
- {
- seqRefs.add(name);
- }
- }
-
- for (String seqRef : seqRefs)
- {
- queryBuilder.append("text:").append(seqRef).append(" OR ");
- }
- }
-
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- if (queryBuilder.toString().length() < 6)
- {
- return null;
- }
- String query = queryBuilder.toString().substring(0, endIndex);
- return query;
- }
-
- /**
- * Remove the following special characters from input string +, -, &, !, (, ),
- * {, }, [, ], ^, ", ~, *, ?, :, \
- *
- * @param seqName
- * @return
- */
- static String sanitizeSeqName(String seqName)
- {
- Objects.requireNonNull(seqName);
- return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
- }
-
-
- /**
- * Ensures sequence ref names are not less than 3 characters and does not
- * contain a database name
- *
- * @param seqName
- * @return
- */
- public static boolean isValidSeqName(String seqName)
- {
- // System.out.println("seqName : " + seqName);
- String ignoreList = "pdb,uniprot,swiss-prot";
- if (seqName.length() < 3)
- {
- return false;
- }
- if (seqName.contains(":"))
- {
- return false;
- }
- seqName = seqName.toLowerCase();
- for (String ignoredEntry : ignoreList.split(","))
- {
- if (seqName.contains(ignoredEntry))
- {
- return false;
- }
- }
- return true;
- }
-
- public static String getDBRefId(DBRefEntry dbRef)
- {
- String ref = dbRef.getAccessionId().replaceAll("GO:", "");
- return ref;
- }
-
- /**
- * Filters a given list of discovered structures based on supplied argument
- *
- * @param fieldToFilterBy
- * the field to filter by
- */
- public void filterResultSet(final String fieldToFilterBy)
- {
- Thread filterThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
- lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
- .getStructureSummaryFields();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
-
- for (SequenceI seq : selectedSequences)
- {
- FTSRestRequest pdbRequest = new FTSRestRequest();
- if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- pdbRequest.setFacet(true);
- pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
- pdbRequest.setFacetPivotMinCount(1);
- }
- else
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- }
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- e.printStackTrace();
- errors.add(e.getMessage());
- continue;
- }
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
- }
-
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- if (!filteredResponse.isEmpty())
- {
- final int filterResponseCount = filteredResponse.size();
- Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
- reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(
- FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
-
- FTSRestResponse.configureTableColumn(getResultTable(),
- wantedFields);
- getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
- getResultTable().getColumn("Ref Sequence").setMinWidth(100);
- getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
- // Update table selection model here
- getResultTable().addRowSelectionInterval(0,
- filterResponseCount - 1);
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time", totalTime));
- }
- else
- {
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time", totalTime));
- if (errors.size() > 0)
- {
- StringBuilder errorMsg = new StringBuilder();
- for (String error : errors)
- {
- errorMsg.append(error).append("\n");
- }
- JOptionPane.showMessageDialog(
- null,
- errorMsg.toString(),
- MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
-
- lbl_loading.setVisible(false);
-
- validateSelections();
- }
- });
- filterThread.start();
- }
-
- /**
- * Handles action event for btn_pdbFromFile
- */
- @Override
- public void pdbFromFile_actionPerformed()
- {
- 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.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence",
- selectedSequence.getDisplayId(false)));
-
- int value = chooser.showOpenDialog(null);
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
- validateSelections();
- }
- }
-
- /**
- * Populates the filter combo-box options dynamically depending on discovered
- * structures
- */
- @Override
- protected void populateFilterComboBox()
- {
- if (isStructuresDiscovered())
- {
- cmb_filterOption.addItem(new FilterOption("Best Quality",
- "overall_quality", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
- }
- cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB));
- }
-
- /**
- * Updates the displayed view based on the selected filter option
- */
- @Override
- protected void updateCurrentView()
- {
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- layout_switchableViews.show(pnl_switchableViews,
- selectedFilterOpt.getView());
- String filterTitle = mainFrame.getTitle();
- mainFrame.setTitle(frameTitle);
- chk_invertFilter.setVisible(false);
- if (selectedFilterOpt.getView() == VIEWS_FILTER)
- {
- mainFrame.setTitle(filterTitle);
- chk_invertFilter.setVisible(true);
- filterResultSet(selectedFilterOpt.getValue());
- }
- else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
- || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
- {
- mainFrame.setTitle(MessageManager
- .getString("label.structure_chooser_manual_association"));
- idInputAssSeqPanel.loadCmbAssSeq();
- fileChooserAssSeqPanel.loadCmbAssSeq();
- }
- validateSelections();
- }
-
- /**
- * Validates user selection and activates the view button if all parameters
- * are correct
- */
- @Override
- public void validateSelections()
- {
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- btn_view.setEnabled(false);
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
- if (getResultTable().getSelectedRows().length > 0)
- {
- btn_view.setEnabled(true);
- }
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- if (tbl_local_pdb.getSelectedRows().length > 0)
- {
- btn_view.setEnabled(true);
- }
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- validateAssociationEnterPdb();
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- validateAssociationFromFile();
- }
- }
-
- /**
- * Validates inputs from the Manual PDB entry panel
- */
- public void validateAssociationEnterPdb()
- {
- AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem();
- lbl_pdbManualFetchStatus.setIcon(errorImage);
- 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())));
- }
-
- if (errorWarning.length() > 0)
- {
- lbl_pdbManualFetchStatus.setIcon(warningImage);
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, errorWarning.toString()));
- }
-
- if (selectedSequences.length == 1
- || !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-"))
- {
- txt_search.setEnabled(true);
- if (isValidPBDEntry)
- {
- btn_view.setEnabled(true);
- lbl_pdbManualFetchStatus.setToolTipText("");
- lbl_pdbManualFetchStatus.setIcon(goodImage);
- }
- }
- else
- {
- txt_search.setEnabled(false);
- lbl_pdbManualFetchStatus.setIcon(errorImage);
- }
- }
-
- /**
- * Validates inputs for the manual PDB file selection options
- */
- public void validateAssociationFromFile()
- {
- AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem();
- lbl_fromFileStatus.setIcon(errorImage);
- if (selectedSequences.length == 1
- || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-")))
- {
- btn_pdbFromFile.setEnabled(true);
- if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
- {
- btn_view.setEnabled(true);
- lbl_fromFileStatus.setIcon(goodImage);
- }
- }
- else
- {
- btn_pdbFromFile.setEnabled(false);
- lbl_fromFileStatus.setIcon(errorImage);
- }
- }
-
- @Override
- public void cmbAssSeqStateChanged()
- {
- validateSelections();
- }
-
- /**
- * Handles the state change event for the 'filter' combo-box and 'invert'
- * check-box
- */
- @Override
- protected void stateChanged(ItemEvent e)
- {
- if (e.getSource() instanceof JCheckBox)
- {
- updateCurrentView();
- }
- else
- {
- if (e.getStateChange() == ItemEvent.SELECTED)
- {
- updateCurrentView();
- }
- }
-
- }
-
- /**
- * Handles action event for btn_ok
- */
- @Override
- public void ok_ActionPerformed()
- {
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- 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();
- int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
- SequenceI selectedSeq = (SequenceI) getResultTable()
- .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);
- }
- 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;
- int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
- .getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- 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();
- if (pdbIdStr.split(":").length > 1)
- {
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
- }
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
-
- 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);
-
- launchStructureViewer(ssm,
- new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
- }
- mainFrame.dispose();
- }
- }).start();
- }
-
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
- {
- Objects.requireNonNull(id);
- Objects.requireNonNull(pdbEntries);
- PDBEntry foundEntry = null;
- for (PDBEntry entry : pdbEntries)
- {
- if (entry.getId().equalsIgnoreCase(id))
- {
- return entry;
- }
- }
- return foundEntry;
- }
-
- private void 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 sViewer = new StructureViewer(ssm);
- setProgressBar(null, progressId);
-
- 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<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
- for (SequenceI seq : sequences)
- {
- if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
- {
- 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 = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
- {
- seqWithoutSrcDBRef[x++] = fSeq;
- }
- new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
- setProgressBar("Fetch complete.", progressId); // todo i18n
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
-<<<<<<< Updated upstream
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
-=======
- setProgressBar("Fetching structure data", progressId);
->>>>>>> Stashed changes
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
-<<<<<<< Updated upstream
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
-=======
- setProgressBar(
- "Fetching structure for " + pdbEntriesToView[0].getId(),
- progressId);
->>>>>>> Stashed changes
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- }
-
- /**
- * Populates the combo-box used in associating manually fetched structures to
- * a unique sequence when more than one sequence selection is made.
- */
- @Override
- public void populateCmbAssociateSeqOptions(
- JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
- {
- cmb_assSeq.removeAllItems();
- cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
- null));
- lbl_associateSeq.setVisible(false);
- if (selectedSequences.length > 1)
- {
- for (SequenceI seq : selectedSequences)
- {
- cmb_assSeq.addItem(new AssociateSeqOptions(seq));
- }
- }
- else
- {
- String seqName = selectedSequence.getDisplayId(false);
- seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
- lbl_associateSeq.setText(seqName);
- lbl_associateSeq.setVisible(true);
- cmb_assSeq.setVisible(false);
- }
- }
-
- public boolean isStructuresDiscovered()
- {
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
- }
-
- public Collection<FTSData> getDiscoveredStructuresSet()
- {
- return discoveredStructuresSet;
- }
-
- @Override
- protected void txt_search_ActionPerformed()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
- {
- String searchTerm = txt_search.getText().toLowerCase();
- searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest
-.setSearchTerm(searchTerm + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
- validateSelections();
- }
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
- }
- }
- validateSelections();
- }
- }.start();
- }
-
- @Override
- public void tabRefresh()
- {
- if (selectedSequences != null)
- {
- Thread refreshThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- fetchStructuresMetaData();
- filterResultSet(((FilterOption) cmb_filterOption
- .getSelectedItem()).getValue());
- }
- });
- refreshThread.start();
- }
- }
-
- public class PDBEntryTableModel extends AbstractTableModel
- {
- String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
-
- private List<CachedPDB> pdbEntries;
-
- public PDBEntryTableModel(List<CachedPDB> pdbEntries)
- {
- this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
- }
-
- @Override
- public String getColumnName(int columnIndex)
- {
- return columns[columnIndex];
- }
-
- @Override
- public int getRowCount()
- {
- return pdbEntries.size();
- }
-
- @Override
- public int getColumnCount()
- {
- return columns.length;
- }
-
- @Override
- public boolean isCellEditable(int row, int column)
- {
- return false;
- }
-
- @Override
- public Object getValueAt(int rowIndex, int columnIndex)
- {
- Object value = "??";
- CachedPDB entry = pdbEntries.get(rowIndex);
- switch (columnIndex)
- {
- case 0:
- value = entry.getSequence();
- break;
- case 1:
- value = entry.getPdbEntry();
- break;
- case 2:
- value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
- .getPdbEntry().getChainCode();
- break;
- case 3:
- value = entry.getPdbEntry().getType();
- break;
- case 4:
- value = entry.getPdbEntry().getFile();
- break;
- }
- return value;
- }
-
- @Override
- public Class<?> getColumnClass(int columnIndex)
- {
- return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
- }
-
- public CachedPDB getPDBEntryAt(int row)
- {
- return pdbEntries.get(row);
- }
-
- }
-
- private class CachedPDB
- {
- private SequenceI sequence;
-
- private PDBEntry pdbEntry;
-
- public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
- {
- this.sequence = sequence;
- this.pdbEntry = pdbEntry;
- }
-
- public SequenceI getSequence()
- {
- return sequence;
- }
-
- public PDBEntry getPdbEntry()
- {
- return pdbEntry;
- }
-
- }
-
- private IProgressIndicator progressBar;
-
- @Override
- public void setProgressBar(String message, long id)
- {
- progressBar.setProgressBar(message, id);
- }
-
- @Override
- public void registerHandler(long id, IProgressIndicatorHandler handler)
- {
- progressBar.registerHandler(id, handler);
- }
-
- @Override
- public boolean operationInProgress()
- {
- return progressBar.operationInProgress();
- }
-}
git://source.jalview.org / jalview.git / blobdiff