/*
-
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
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.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+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.Hashtable;
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.DefaultTableModel;
-
+import javax.swing.table.AbstractTableModel;
/**
* Provides the behaviors for the Structure chooser Panel
*/
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
+ implements IProgressIndicator
{
- private boolean structuresDiscovered = false;
+ private static int MAX_QLENGTH = 7820;
private SequenceI selectedSequence;
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet;
+ private Collection<FTSData> discoveredStructuresSet;
- private PDBRestRequest lastPdbRequest;
+ private FTSRestRequest lastPdbRequest;
- private PDBRestClient pdbRestCleint;
+ private FTSRestClientI pdbRestCleint;
private String selectedPdbFileName;
private boolean isValidPBDEntry;
- private static Hashtable<String, PDBEntry> cachedEntryMap;
+ private boolean cachedPDBExists;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
*/
public void init()
{
+ if (!Jalview.isHeadlessMode())
+ {
+ 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
public void run()
{
long startTime = System.currentTimeMillis();
- String msg = MessageManager.getString("status.fetching_db_refs");
- updateProgressIndicator(msg, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager.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();
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
- HashSet<String> errors = new HashSet<String>();
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(text:");
+ 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.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ pdbRequest.setAssociatedSequence(seq);
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
+ e.printStackTrace();
errors.add(e.getMessage());
continue;
}
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequencePDBEntries(seq, resultList.getSearchSummary());
}
}
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
- mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
- + " Found (" + totalTime + ")");
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_no_of_structures",
+ noOfStructuresFound, totalTime));
}
else
{
- mainFrame
-.setTitle("Structure Chooser - Manual association");
+ mainFrame.setTitle(MessageManager
+ .getString("label.structure_chooser_manual_association"));
if (errors.size() > 0)
{
- StringBuilder errorMsg = new StringBuilder(
- "Operation was unsucessful due to the following: \n");
+ StringBuilder errorMsg = new StringBuilder();
for (String error : errors)
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
- "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
public void loadLocalCachedPDBEntries()
{
- DefaultTableModel tableModel = new DefaultTableModel();
- tableModel.addColumn("Sequence");
- tableModel.addColumn("PDB Id");
- tableModel.addColumn("Chain");
- tableModel.addColumn("Type");
- tableModel.addColumn("File");
- cachedEntryMap = new Hashtable<String, PDBEntry>();
+ ArrayList<CachedPDB> entries = new ArrayList<>();
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getPDBId() != null)
+ && seq.getDatasetSequence().getAllPDBEntries() != null)
{
- for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+ for (PDBEntry pdbEntry : seq.getDatasetSequence()
+ .getAllPDBEntries())
{
-
- String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
- .getChainCode();
- String[] pdbEntryRowData = new String[]
- { seq.getDisplayId(false), pdbEntry.getId(),
- chain,
- pdbEntry.getType(),
- pdbEntry.getFile() };
if (pdbEntry.getFile() != null)
{
- tableModel.addRow(pdbEntryRowData);
+ entries.add(new CachedPDB(seq, pdbEntry));
}
- cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
- pdbEntry);
}
}
}
- tbl_local_pdb.setModel(tableModel);
- }
-
- /**
- * Update the PDBEntry for a given sequence with values retrieved from
- * PDBResponseSummary
- *
- * @param seq
- * the Sequence to update its DBRef entry
- * @param responseSummaries
- * a collection of PDBResponseSummary
- */
- public void updateSequencePDBEntries(SequenceI seq,
- Collection<PDBResponseSummary> responseSummaries)
- {
- for (PDBResponseSummary response : responseSummaries)
- {
- String pdbIdStr = response.getPdbId();
- PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- }
- seq.getDatasetSequence().addPDBId(pdbEntry);
- }
+ cachedPDBExists = !entries.isEmpty();
+ PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
+ tbl_local_pdb.setModel(tableModelx);
}
/**
public static String buildQuery(SequenceI seq)
{
- HashSet<String> seqRefs = new LinkedHashSet<String>();
- String seqName = seq.getName();
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
+ boolean isPDBRefsFound = false;
+ boolean isUniProtRefsFound = false;
+ StringBuilder queryBuilder = new StringBuilder();
+ Set<String> seqRefs = new LinkedHashSet<>();
+
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ for (PDBEntry entry : seq.getAllPDBEntries())
{
- seqRefs.add(name);
+ if (isValidSeqName(entry.getId()))
+ {
+ queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
+ .append(" OR ");
+ isPDBRefsFound = true;
+ }
}
}
- if (seq.getPDBId() != null)
+ if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
{
- for (PDBEntry entry : seq.getPDBId())
+ for (DBRefEntry dbRef : seq.getDBRefs())
{
- seqRefs.add(entry.getId());
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ 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(getDBRefId(dbRef).toLowerCase()).append(" OR ");
+ isPDBRefsFound = true;
+ }
+ else
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
+ }
}
}
- if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ if (!isPDBRefsFound && !isUniProtRefsFound)
{
- int count = 0;
- for (DBRefEntry dbRef : seq.getDBRef())
+ String seqName = seq.getName();
+ seqName = sanitizeSeqName(seqName);
+ String[] names = seqName.toLowerCase().split("\\|");
+ for (String name : names)
{
- seqRefs.add(getDBRefId(dbRef));
- ++count;
- if (count > 10)
+ // System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
{
- break;
+ seqRefs.add(name);
}
}
+
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
}
- StringBuilder queryBuilder = new StringBuilder();
- for (String seqRef : seqRefs)
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ if (queryBuilder.toString().length() < 6)
{
- queryBuilder.append("text:").append(seqRef).append(" OR ");
+ return null;
}
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- String query = queryBuilder.toString().substring(5, endIndex);
+ 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
*
*/
public static boolean isValidSeqName(String seqName)
{
- String ignoreList = "pdb,uniprot";
+ // 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.equalsIgnoreCase(ignoredEntry))
+ if (seqName.contains(ignoredEntry))
{
return false;
}
public void run()
{
long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- HashSet<String> errors = new HashSet<String>();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
+
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ 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;
}
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, reorderedStructuresSet));
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
+ getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+ getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+ getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
// Update table selection model here
- tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
-
- mainFrame.setTitle("Structure Chooser - Filter time ("
- + totalTime + ")");
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
}
else
{
- mainFrame.setTitle("Structure Chooser - Filter time ("
- + totalTime + ")");
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
if (errors.size() > 0)
{
- StringBuilder errorMsg = new StringBuilder(
- "Operation unsucessful due to the following: \n");
+ StringBuilder errorMsg = new StringBuilder();
for (String error : errors)
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(null, errorMsg.toString(),
- "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
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", new String[]
- { 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", new String[]
- { selectedSequence.getDisplayId(false) }));
+ "label.load_pdb_file_associate_with_sequence",
+ selectedSequence.getDisplayId(false)));
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- protected void populateFilterComboBox()
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist)
{
- if (isStructuresDiscovered())
- {
- cmb_filterOption.addItem(new FilterOption("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
- PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
- PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
- PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
- PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), 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));
+ /*
+ * temporarily suspend the change listener behaviour
+ */
+ cmb_filterOption.removeItemListener(this);
+
+ cmb_filterOption.removeAllItems();
+ if (haveData)
+ {
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_polymer_residues"),
+ "number_of_polymer_residues", VIEWS_FILTER, true));
+ }
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.enter_pdb_id"),
+ "-", VIEWS_ENTER_ID, false));
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.from_file"),
+ "-", VIEWS_FROM_FILE, false));
+
+ if (cachedPDBExist)
+ {
+ FilterOption cachedOption = new FilterOption(
+ MessageManager.getString("label.cached_structures"),
+ "-", VIEWS_LOCAL_PDB, false);
+ cmb_filterOption.addItem(cachedOption);
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+
+ cmb_filterOption.addItemListener(this);
}
/**
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
- mainFrame.setTitle(filterTitle);
+ mainFrame.setTitle(MessageManager
+ .getString("label.structure_chooser_manual_association"));
idInputAssSeqPanel.loadCmbAssSeq();
fileChooserAssSeqPanel.loadCmbAssSeq();
}
* Validates user selection and activates the view button if all parameters
* are correct
*/
+ @Override
public void validateSelections()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- if (tbl_summary.getSelectedRows().length > 0)
+ if (getResultTable().getSelectedRows().length > 0)
{
btn_view.setEnabled(true);
}
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_pdbManualFetchStatus.setIcon(errorImage);
- if (selectedSequences.length == 1
- || !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-"))
+ 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);
}
}
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)
@Override
public void ok_ActionPerformed()
{
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
+ final int preferredHeight = pnl_filter.getHeight();
+
+ new Thread(new Runnable()
{
- int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
- lastPdbRequest.getWantedFields(), true);
- int[] selectedRows = tbl_summary.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- for (int summaryRow : selectedRows)
+ @Override
+ public void run()
{
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
+ 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;
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ 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());
+ }
- PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
- if (pdbEntry == null)
+ 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)
{
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.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();
+ List<SequenceI> 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);
}
- pdbEntriesToView[count++] = pdbEntry;
- }
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSequences);
- }
- else if(currentView == VIEWS_LOCAL_PDB){
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- for (int row : selectedRows)
- {
- String entryKey = tbl_local_pdb.getValueAt(row, 1).toString()
- .toLowerCase();
- pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
- }
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSequences);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ 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.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(txt_search.getText());
- pdbEntry.setType(PDBEntry.Type.PDB);
+ 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,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+
+ launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[]
+ { selectedSequence });
+ }
+ closeAction(preferredHeight);
+ mainFrame.dispose();
}
+ }).start();
+ }
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- PDBEntry[] pdbEntriesToView = new PDBEntry[]
- { pdbEntry };
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, new SequenceI[]
- { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
+ private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
{
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
+ if (entry.getId().equalsIgnoreCase(id))
{
- selectedSequence = userSelectedSeq;
+ return entry;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(
- selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
-
- launchStructureViewer(ap.getStructureSelectionManager(),
- new PDBEntry[]
- { fileEntry }, ap, new SequenceI[]
- { selectedSequence });
}
- mainFrame.dispose();
+ return foundEntry;
}
private void launchStructureViewer(StructureSelectionManager ssm,
- PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- StructureViewer sViewer = new StructureViewer(ssm);
+ 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<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().size() == 0)
+ {
+ 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;
+ }
+
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
if (pdbEntriesToView.length > 1)
{
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
+ setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
}
else
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
- alignPanel);
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ 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)
+ JComboBox<AssociateSeqOptions> cmb_assSeq,
+ JLabel lbl_associateSeq)
{
cmb_assSeq.removeAllItems();
- cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
- null));
- // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", null));
lbl_associateSeq.setVisible(false);
if (selectedSequences.length > 1)
{
public boolean isStructuresDiscovered()
{
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
- public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ public Collection<FTSData> getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
@Override
protected void txt_search_ActionPerformed()
{
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
+ new Thread()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- JOptionPane.showMessageDialog(this, e.getMessage(),
- "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
- return;
- } finally
+ @Override
+ public void run()
{
- System.out.println(">>>>> executing finally block");
+ 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<>();
+ 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();
}
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
- }
- }
- validateSelections();
+ }.start();
}
@Override
public void run()
{
fetchStructuresMetaData();
- filterResultSet(((FilterOption) cmb_filterOption
- .getSelectedItem()).getValue());
+ 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<>(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