X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=7c386f1a8cf63bd953e20adcaa2d22f2b871ae83;hb=bf97c293ad31f6ed5006a97d3a7d079c032652e8;hp=07e36ec7b4f3bd3d8c9986725d28a767490513ea;hpb=7d76e402efd4e04e179bc9bb264551bc2d3df936;p=jalview.git
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 07e36ec..7c386f1 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,273 +1,1173 @@
+/*
+ * 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 .
+ * 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.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSummaryListModel;
-import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+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.Set;
+import java.util.Vector;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+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 static int MAX_QLENGTH = 7820;
+
+ private SequenceI selectedSequence;
+
+ private SequenceI[] selectedSequences;
+
+ private IProgressIndicator progressIndicator;
+
+ private Collection discoveredStructuresSet;
+ private FTSRestRequest lastPdbRequest;
- private SequenceI sequence;
+ private FTSRestClientI pdbRestCleint;
+ private String selectedPdbFileName;
- public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+ private boolean isValidPBDEntry;
+
+ private boolean cachedPDBExists;
+
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap)
{
this.ap = ap;
- this.sequence = sequence;
- fetchStructures();
+ this.selectedSequence = selectedSeq;
+ this.selectedSequences = selectedSeqs;
+ this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+ init();
}
- @Override
- public void ok_ActionPerformed()
+ /**
+ * Initializes parameters used by the Structure Chooser Panel
+ */
+ 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();
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
+ loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager.getString(
+ "status.searching_for_pdb_structures"), startTime);
+ fetchStructuresMetaData();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ 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 wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet errors = new HashSet<>();
+ for (SequenceI seq : selectedSequences)
+ {
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ 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);
+ 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));
+ 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");
+ }
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+
+ public void loadLocalCachedPDBEntries()
+ {
+ ArrayList entries = new ArrayList<>();
+ 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));
+ }
+ }
+ }
+ }
+ cachedPDBExists = !entries.isEmpty();
+ 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();
+ Set seqRefs = new LinkedHashSet<>();
+
+ 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 ");
+ isPDBRefsFound = true;
+ }
+ }
+ }
+
+ if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
+ {
+ for (DBRefEntry dbRef : seq.getDBRefs())
+ {
+ 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 (!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)
{
- jListFoundStructures.setSelectedValue("op1x", true);
+ 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 wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+ Collection filteredResponse = new HashSet<>();
+ HashSet errors = new HashSet<>();
+
+ 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 reorderedStructuresSet = new LinkedHashSet<>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ 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
+ 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");
+ }
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.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", new String[]
- { sequence.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[]
- { sequence.getDisplayId(false) }));
+ "label.load_pdb_file_associate_with_sequence",
+ selectedSequence.getDisplayId(false)));
int value = chooser.showOpenDialog(null);
-
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true,
- Desktop.instance);
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
+ }
+ }
+
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExists)
+ {
+ /*
+ * 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, false));
+ cmb_filterOption.addItem(new FilterOption("Best Resolution",
+ "resolution", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
+ "number_of_protein_chains", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
+ "number_of_bound_molecules", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
+ "number_of_polymer_residues", VIEWS_FILTER, true));
}
+ 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);
+ }
+
+ cmb_filterOption.addItemListener(this);
}
- public void discoverPDB_actionPerformed()
+ /**
+ * Updates the displayed view based on the selected filter option
+ */
+ 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();
+ }
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- Thread discpdb = new Thread(new Runnable()
+ /**
+ * 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)
{
- @Override
- public void run()
+ 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()));
+ }
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
+ 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);
+ }
+ }
- });
- discpdb.start();
+ /**
+ * 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);
+ }
}
- // rpdbview.addActionListener(new ActionListener()
- // {
- //
- // @Override
- // public void actionPerformed(ActionEvent e)
- // {
- // new StructureViewer(ap.getStructureSelectionManager())
- // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- // }
- // });
-
- public void enterPDB_actionPerformed()
+ @Override
+ public void cmbAssSeqStateChanged()
{
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"),
- MessageManager.getString("label.enter_pdb_id"),
- JOptionPane.QUESTION_MESSAGE);
- if (id != null && id.length() > 0)
+ 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
{
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
}
+
}
- public static void main(String[] args)
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
{
- SwingUtilities.invokeLater(new Runnable()
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
+ final int preferredHeight = pnl_filter.getHeight();
+
+ new Thread(new Runnable()
{
+ @Override
public void run()
{
- new StructureChooser(null, null);
+ 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 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());
+ }
+
+ 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();
+ List selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ 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);
+ }
+
+ 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();
}
- @SuppressWarnings("unchecked")
- protected void populateFilterOptions()
+ private PDBEntry getFindEntry(String id, Vector pdbEntries)
{
- filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
- VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Best Resolution", "",
- VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
- filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
}
- protected void updateCurrentView()
+ private void launchStructureViewer(StructureSelectionManager ssm,
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- String currentView = ((FilterOptions) filterOptions.getSelectedItem())
- .getView();
- switchableViewsLayout.show(switchableViewsPanel, currentView);
+ 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<>();
+ 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)
+ {
+ setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ }
+ else
+ {
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
+ setProgressBar(null, progressId);
}
- private void fetchStructures()
+ /**
+ * 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 cmb_assSeq,
+ JLabel lbl_associateSeq)
{
- long startTime = System.currentTimeMillis();
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- int foundStructures = 0;
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(500);
- request.setSearchTarget("(text:");
- List wantedFields = new ArrayList();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
- request.setWantedFields(wantedFields);
-
- Collection searchSummaries = new HashSet();
- // searchSummaries.
- for (SequenceI seq : sequences)
- {
- // System.out.println("Selected : " + seq.getName());
- request.setSearchTerm(buildQuery(seq) + ")");
-
- PDBRestClient pdbRestCleint = new PDBRestClient();
-
- PDBSearchResponse resultList = pdbRestCleint
- .executeRequest(request);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", null));
+ lbl_associateSeq.setVisible(false);
+ if (selectedSequences.length > 1)
+ {
+ for (SequenceI seq : selectedSequences)
{
- searchSummaries.addAll(resultList.getSearchSummary());
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
}
}
-
- foundStructures = searchSummaries.size();
- if (searchSummaries != null)
+ else
{
- jListFoundStructures.setModel(PDBSearchResponse
- .getListModel(searchSummaries));
+ 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);
}
+ }
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + foundStructures
- + " Found (" + totalTime + ")");
+ public boolean isStructuresDiscovered()
+ {
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
- private String buildQuery(SequenceI seq)
+ public Collection getDiscoveredStructuresSet()
{
- String query = seq.getName();
- StringBuilder queryBuilder = new StringBuilder();
- int count = 0;
- if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ return discoveredStructuresSet;
+ }
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ new Thread()
{
- for (DBRefEntry dbRef : seq.getDBRef())
+ @Override
+ public void run()
{
- System.out.println("dbref : " + dbRef.getAccessionId());
- queryBuilder.append("text:").append(dbRef.getAccessionId())
- .append(" OR ");
- ++count;
- if (count > 10)
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
{
- break;
+ String searchTerm = txt_search.getText().toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
+ List 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();
}
- // int beginIndex = queryBuilder. firstIndexOf("text");
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- query = queryBuilder.toString().substring(5, endIndex);
+ }.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();
}
- System.out.println("------------> " + query);
- return query;
}
- public class FilterOptions
+ public class PDBEntryTableModel extends AbstractTableModel
{
- private String name;
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
+
+ private List pdbEntries;
- private String value;
+ public PDBEntryTableModel(List pdbEntries)
+ {
+ this.pdbEntries = new ArrayList<>(pdbEntries);
+ }
- private String view;
+ @Override
+ public String getColumnName(int columnIndex)
+ {
+ return columns[columnIndex];
+ }
- public FilterOptions(String name, String value, String view)
+ @Override
+ public int getRowCount()
{
- this.name = name;
- this.value = value;
- this.view = view;
+ return pdbEntries.size();
}
- public String getName()
+ @Override
+ public int getColumnCount()
{
- return name;
+ return columns.length;
}
- public void setName(String name)
+ @Override
+ public boolean isCellEditable(int row, int column)
{
- this.name = name;
+ return false;
}
- public String getValue()
+ @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;
}
- public void setValue(String value)
+ @Override
+ public Class getColumnClass(int columnIndex)
{
- this.value = value;
+ return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
}
- public String getView()
+ public CachedPDB getPDBEntryAt(int row)
{
- return view;
+ return pdbEntries.get(row);
}
- public void setView(String view)
+ }
+
+ private class CachedPDB
+ {
+ private SequenceI sequence;
+
+ private PDBEntry pdbEntry;
+
+ public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
{
- this.view = view;
+ this.sequence = sequence;
+ this.pdbEntry = pdbEntry;
}
- public String toString()
+ public SequenceI getSequence()
{
- return this.name;
+ 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();
}
}