package jalview.gui;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+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.Locale;
+import java.util.concurrent.Executors;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
+
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
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.FTSDataColumnPreferences;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.jbgui.FilterOption;
import jalview.jbgui.GStructureChooser;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.seqfetcher.DbSourceProxy;
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.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
*
*
*/
@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser implements
- IProgressIndicator
+public class StructureChooser extends GStructureChooser
+ implements IProgressIndicator
{
- private static int MAX_QLENGTH = 7820;
+ protected static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+ /**
+ * warn user if need to fetch more than this many uniprot records at once
+ */
+ private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private Collection<FTSData> discoveredStructuresSet;
- private FTSRestRequest lastPdbRequest;
+ private StructureChooserQuerySource data;
- private FTSRestClientI pdbRestCleint;
+ @Override
+ protected FTSDataColumnPreferences getFTSDocFieldPrefs()
+ {
+ return data.getDocFieldPrefs();
+ }
private String selectedPdbFileName;
private boolean cachedPDBExists;
+ private Collection<FTSData> lastDiscoveredStructuresSet;
+
+ private boolean canQueryTDB = false;
+
+ private boolean notQueriedTDBYet = true;
+
+ List<SequenceI> seqsWithoutSourceDBRef = null;
+
+ protected static StructureViewer lastTargetedView = null;
+
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
+ // which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
+ initDialog();
+
this.ap = ap;
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
+
}
/**
+ * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
+ * least one structure are discovered.
+ */
+ private void populateSeqsWithoutSourceDBRef()
+ {
+ seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ boolean needCanonical = false;
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.isProtein())
+ {
+ int dbRef = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (dbRef < 0)
+ {
+ if (dbRef == -1)
+ {
+ // need to retrieve canonicals
+ needCanonical = true;
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ else
+ {
+ // could be a sequence with pdb ref
+ if (seq.getAllPDBEntries() == null
+ || seq.getAllPDBEntries().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ }
+ }
+ // retrieve database refs for protein sequences
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ canQueryTDB = true;
+ if (needCanonical)
+ {
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
+ }
+ }
+ };
+
+ /**
* Initializes parameters used by the Structure Chooser Panel
*/
- public void init()
+ protected void init()
{
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+ btn_queryTDB.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ promptForTDBFetch(false);
+ }
+ });
+
+ Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ populateSeqsWithoutSourceDBRef();
+ initialStructureDiscovery();
+ }
+
+ }).start();
+
+ }
+
+ // called by init
+ private void initialStructureDiscovery()
+ {
+ // check which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
+
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
+
+ // looks for any existing structures already loaded
+ // for the sequences (the cached ones)
+ // then queries the StructureChooserQuerySource to
+ // discover more structures.
+ //
+ // Possible optimisation is to only begin querying
+ // the structure chooser if there are no cached structures.
+
+ 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);
+ discoverStructureViews();
+ updateProgressIndicator(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ *
+ * @param ignoreGui
+ * - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
+ {
+ final long progressId = System.currentTimeMillis();
+
+ // final action after prompting and discovering db refs
+ final Runnable strucDiscovery = 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();
+ mainFrame.setEnabled(false);
+ cmb_filterOption.setEnabled(false);
+ progressBar.setProgressBar(
+ MessageManager.getString("status.searching_3d_beacons"),
+ progressId);
+ btn_queryTDB.setEnabled(false);
+ // TODO: warn if no accessions discovered
+ populateSeqsWithoutSourceDBRef();
+ // redo initial discovery - this time with 3d beacons
+ // Executors.
+ previousWantedFields = null;
+ lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
+ initialStructureDiscovery();
+ if (!isStructuresDiscovered())
+ {
+ progressBar.setProgressBar(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"),
+ progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"));
+ btn_queryTDB.setEnabled(false);
+ pnl_queryTDB.setVisible(false);
+ }
+ else
+ {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
+ btn_queryTDB.setVisible(false);
+ pnl_queryTDB.setVisible(false);
+ progressBar.setProgressBar(null, progressId);
+ }
+ mainFrame.setEnabled(true);
+ cmb_filterOption.setEnabled(true);
}
- });
- discoverPDBStructuresThread.start();
+ };
+
+ final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
+ {
+
+ @Override
+ public void finished()
+ {
+ // filter has been selected, so we set flag to remove ourselves
+ notQueriedTDBYet = false;
+ // new thread to discover structures - via 3d beacons
+ Executors.defaultThreadFactory().newThread(strucDiscovery).start();
+
+ }
+ };
+
+ // fetch db refs if OK pressed
+ final Runnable discoverCanonicalDBrefs = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ btn_queryTDB.setEnabled(false);
+ populateSeqsWithoutSourceDBRef();
+
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
+ {
+ final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() }, null, false);
+ dbRefFetcher.addListener(afterDbRefFetch);
+ // ideally this would also gracefully run with callbacks
+ dbRefFetcher.fetchDBRefs(true);
+ }
+ else
+ {
+ // call finished action directly
+ afterDbRefFetch.finished();
+ }
+ }
+
+ };
+ final Runnable revertview = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (lastSelected != null)
+ {
+ cmb_filterOption.setSelectedItem(lastSelected);
+ }
+ };
+ };
+ int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
+ THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
+ Console.debug("Using Uniprot fetch threshold of " + threshold);
+ if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
+ // need cancel and no to result in the discoverPDB action - mocked is
+ // 'cancel' TODO: mock should be OK
+ StructureChooser thisSC = this;
+ JvOptionPane.newOptionDialog(thisSC.getFrame())
+ .setResponseHandler(JvOptionPane.OK_OPTION,
+ discoverCanonicalDBrefs)
+ .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
+ .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
+ .showDialog(
+ MessageManager.formatMessage(
+ "label.fetch_references_for_3dbeacons",
+ seqsWithoutSourceDBRef.size()),
+ MessageManager
+ .getString("label.3dbeacons"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
+ null, new Object[]
+ { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.ok"), false);
+ }
+
+ /**
+ * Builds a drop-down choice list of existing structure viewers to which new
+ * structures may be added. If this list is empty then it, and the 'Add'
+ * button, are hidden.
+ */
+ private void discoverStructureViews()
+ {
+ if (Desktop.getInstance() != null)
+ {
+ targetView.removeAllItems();
+ if (lastTargetedView != null && !lastTargetedView.isVisible())
+ {
+ lastTargetedView = null;
+ }
+ int linkedViewsAt = 0;
+ for (StructureViewerBase view : Desktop.getInstance()
+ .getStructureViewers(null, null))
+ {
+ StructureViewer viewHandler = (lastTargetedView != null
+ && lastTargetedView.sview == view) ? lastTargetedView
+ : StructureViewer.reconfigure(view);
+
+ if (view.isLinkedWith(ap))
+ {
+ targetView.insertItemAt(viewHandler, linkedViewsAt++);
+ }
+ else
+ {
+ targetView.addItem(viewHandler);
+ }
+ }
+
+ /*
+ * show option to Add to viewer if at least 1 viewer found
+ */
+ targetView.setVisible(false);
+ if (targetView.getItemCount() > 0)
+ {
+ targetView.setVisible(true);
+ if (lastTargetedView != null)
+ {
+ targetView.setSelectedItem(lastTargetedView);
+ }
+ else
+ {
+ targetView.setSelectedIndex(0);
+ }
+ }
+ btn_add.setVisible(targetView.isVisible());
+ }
}
/**
* @param id
* unique handle for this indicator
*/
- public void updateProgressIndicator(String message, long id)
+ protected void updateProgressIndicator(String message, long id)
{
if (progressIndicator != null)
{
* Retrieve meta-data for all the structure(s) for a given sequence(s) in a
* selection group
*/
- public void fetchStructuresMetaData()
+ void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> errors = new HashSet<>();
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+
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);
+ resultList = data.fetchStructuresMetaData(seq, wantedFields,
+ selectedFilterOpt, !chk_invertFilter.isSelected());
+ // null response means the FTSengine didn't yield a query for this
+ // consider designing a special exception if we really wanted to be
+ // OOCrazy
+ if (resultList == null)
+ {
+ continue;
+ }
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(discoveredStructuresSet));
+
noOfStructuresFound = discoveredStructuresSet.size();
+ lastDiscoveredStructuresSet = discoveredStructuresSet;
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
noOfStructuresFound, totalTime));
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
- public void loadLocalCachedPDBEntries()
+ protected void loadLocalCachedPDBEntries()
{
- ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
+ ArrayList<CachedPDB> entries = new ArrayList<>();
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
}
/**
- * 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<String> seqRefs = new LinkedHashSet<String>();
-
- 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)
- {
- 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)
+ 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
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> 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);
+ resultList = data.selectFirstRankedQuery(seq,
+ discoveredStructuresSet, wantedFields, fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- reorderedStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
- null,
- errorMsg.toString(),
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
* Handles action event for btn_pdbFromFile
*/
@Override
- public void pdbFromFile_actionPerformed()
+ protected void pdbFromFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
+ // StructureChooser
+ // works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for",
- selectedSequence.getDisplayId(false)));
+ chooser.setDialogTitle(
+ MessageManager.formatMessage("label.select_pdb_file_for",
+ selectedSequence.getDisplayId(false)));
chooser.setToolTipText(MessageManager.formatMessage(
"label.load_pdb_file_associate_with_sequence",
selectedSequence.getDisplayId(false)));
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
* structures
*/
protected void populateFilterComboBox(boolean haveData,
- boolean cachedPDBExists)
+ boolean cachedPDBExist)
{
+ populateFilterComboBox(haveData, cachedPDBExist, null);
+ }
+
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist, FilterOption lastSel)
+ {
+
/*
* temporarily suspend the change listener behaviour
*/
cmb_filterOption.removeItemListener(this);
-
+ int selSet = -1;
cmb_filterOption.removeAllItems();
if (haveData)
{
- 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));
+ List<FilterOption> filters = data
+ .getAvailableFilterOptions(VIEWS_FILTER);
+ data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
+ lastDiscoveredStructuresSet);
+ int p = 0;
+ for (FilterOption filter : filters)
+ {
+ if (lastSel != null && filter.equals(lastSel))
+ {
+ selSet = p;
+ }
+ p++;
+ cmb_filterOption.addItem(filter);
+ }
}
- cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB);
- cmb_filterOption.addItem(cachedOption);
-
- if (/*!haveData &&*/cachedPDBExists)
+
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.enter_pdb_id"),
+ "-", VIEWS_ENTER_ID, false, null));
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.from_file"),
+ "-", VIEWS_FROM_FILE, false, null));
+ if (canQueryTDB && notQueriedTDBYet)
{
- cmb_filterOption.setSelectedItem(cachedOption);
+ btn_queryTDB.setVisible(true);
+ pnl_queryTDB.setVisible(true);
}
+ if (cachedPDBExist)
+ {
+ FilterOption cachedOption = new FilterOption(
+ MessageManager.getString("label.cached_structures"), "-",
+ VIEWS_LOCAL_PDB, false, null);
+ cmb_filterOption.addItem(cachedOption);
+ if (selSet == -1)
+ {
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+ }
+ if (selSet > -1)
+ {
+ cmb_filterOption.setSelectedIndex(selSet);
+ }
cmb_filterOption.addItemListener(this);
}
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
+
+ if (lastSelected == selectedFilterOpt)
+ {
+ // don't need to do anything, probably
+ return;
+ }
+ // otherwise, record selection
+ // and update the layout and dialog accordingly
+ lastSelected = selectedFilterOpt;
+
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());
+ // TDB Query has no invert as yet
+ chk_invertFilter.setVisible(selectedFilterOpt
+ .getQuerySource() instanceof PDBStructureChooserQuerySource);
+
+ if (data != selectedFilterOpt.getQuerySource()
+ || data.needsRefetch(selectedFilterOpt))
+ {
+ data = selectedFilterOpt.getQuerySource();
+ // rebuild the views completely, since prefs will also change
+ tabRefresh();
+ return;
+ }
+ else
+ {
+ filterResultSet(selectedFilterOpt.getValue());
+ }
}
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
}
/**
- * Validates user selection and activates the view button if all parameters
- * are correct
+ * Validates user selection and enables the 'Add' and 'New View' buttons if
+ * all parameters are correct (the Add button will only be visible if there is
+ * at least one existing structure viewer open). This basically means at least
+ * one structure selected and no error messages.
+ * <p>
+ * The 'Superpose Structures' option is enabled if either more than one
+ * structure is selected, or the 'Add' to existing view option is enabled, and
+ * disabled if the only option is to open a new view of a single structure.
*/
@Override
- public void validateSelections()
+ protected void validateSelections()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
- btn_view.setEnabled(false);
+ btn_add.setEnabled(false);
String currentView = selectedFilterOpt.getView();
+ int selectedCount = 0;
if (currentView == VIEWS_FILTER)
{
- if (getResultTable().getSelectedRows().length > 0)
+ selectedCount = getResultTable().getSelectedRows().length;
+ if (selectedCount > 0)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
}
}
else if (currentView == VIEWS_LOCAL_PDB)
{
- if (tbl_local_pdb.getSelectedRows().length > 0)
+ selectedCount = tbl_local_pdb.getSelectedRows().length;
+ if (selectedCount > 0)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
}
}
else if (currentView == VIEWS_ENTER_ID)
{
validateAssociationFromFile();
}
+
+ btn_newView.setEnabled(btn_add.isEnabled());
+
+ /*
+ * enable 'Superpose' option if more than one structure is selected,
+ * or there are view(s) available to add structure(s) to
+ */
+ chk_superpose
+ .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
}
+ @Override
+ protected boolean showPopupFor(int selectedRow, int x, int y)
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER
+ && data instanceof ThreeDBStructureChooserQuerySource)
+ {
+ TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
+ .getFTSDataFor(getResultTable(), selectedRow,
+ discoveredStructuresSet);
+ String pageUrl = row.getModelViewUrl();
+ JPopupMenu popup = new JPopupMenu("3D Beacons");
+ JMenuItem viewUrl = new JMenuItem("View model web page");
+ viewUrl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ });
+ popup.add(viewUrl);
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ popup.show(getResultTable(), x, y);
+ }
+ });
+ return true;
+ }
+ // event not handled by us
+ return false;
+ }
/**
* Validates inputs from the Manual PDB entry panel
*/
- public void validateAssociationEnterPdb()
+ protected void validateAssociationEnterPdb()
{
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_pdbManualFetchStatus.setToolTipText("");
if (txt_search.getText().length() > 0)
{
- lbl_pdbManualFetchStatus
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .formatMessage("info.no_pdb_entry_found_for",
- txt_search.getText())));
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("info.no_pdb_entry_found_for",
+ txt_search.getText())));
}
if (errorWarning.length() > 0)
{
lbl_pdbManualFetchStatus.setIcon(warningImage);
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, errorWarning.toString()));
+ lbl_pdbManualFetchStatus.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
}
- if (selectedSequences.length == 1
- || !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-"))
+ if (selectedSequences.length == 1 || !assSeqOpt.getName()
+ .equalsIgnoreCase("-Select Associated Seq-"))
{
txt_search.setEnabled(true);
if (isValidPBDEntry)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
lbl_pdbManualFetchStatus.setToolTipText("");
lbl_pdbManualFetchStatus.setIcon(goodImage);
}
/**
* Validates inputs for the manual PDB file selection options
*/
- public void validateAssociationFromFile()
+ protected 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-")))
+ 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);
+ btn_add.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
}
@Override
- public void cmbAssSeqStateChanged()
+ protected void cmbAssSeqStateChanged()
{
validateSelections();
}
-
+ private FilterOption lastSelected=null;
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
}
/**
- * Handles action event for btn_ok
+ * select structures for viewing by their PDB IDs
+ *
+ * @param pdbids
+ * @return true if structures were found and marked as selected
+ */
+ public boolean selectStructure(String... pdbids)
+ {
+ boolean found = false;
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
+
+ if (restable == null)
+ {
+ // can't select (enter PDB ID, or load file - need to also select which
+ // sequence to associate with)
+ return false;
+ }
+
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+ for (int r = 0; r < restable.getRowCount(); r++)
+ {
+ for (int p = 0; p < pdbids.length; p++)
+ {
+ if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+ .equalsIgnoreCase(pdbids[p]))
+ {
+ restable.setRowSelectionInterval(r, r);
+ found = true;
+ }
+ }
+ }
+ return found;
+ }
+
+ /**
+ * Handles the 'New View' action
+ */
+ @Override
+ protected void newView_ActionPerformed()
+ {
+ targetView.setSelectedItem(null);
+ showStructures(false);
+ }
+
+ /**
+ * Handles the 'Add to existing viewer' action
*/
@Override
- public void ok_ActionPerformed()
+ protected void add_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
+ showStructures(false);
+ }
+
+ /**
+ * structure viewer opened by this dialog, or null
+ */
+ private StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+ boolean superimpose = chk_superpose.isSelected();
final int preferredHeight = pnl_filter.getHeight();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
- new Thread(new Runnable()
+
+ Runnable viewStruc = new Runnable()
{
@Override
public void run()
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : tbl_local_pdb;
+
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = getResultTable().getColumn("PDB Id")
- .getModelIndex();
- int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
- int[] selectedRows = getResultTable().getSelectedRows();
+ int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- List<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;
- }
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ pdbEntriesToView = data.collectSelectedRows(restable,
+ selectedRows, selectedSeqsToView);
+
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
.getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
- List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+ .getModel()).getPDBEntryAt(row).getPdbEntry();
+
pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
- row, refSeqColIndex);
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb
+ .getValueAt(row, refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_ENTER_ID)
{
{
selectedSequence = userSelectedSeq;
}
-
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
- pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
}
else
{
}
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 });
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ new SequenceI[]
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
- closeAction(preferredHeight);
- }
- }).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)
- {
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
- final StructureViewer sViewer = new StructureViewer(ssm);
-
- if (SiftsSettings.isMapWithSifts())
- {
- List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
- 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)
+ else if (currentView == VIEWS_FROM_FILE)
{
- StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
- if (smm != null && smm.length > 0)
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
{
- for (StructureMapping sm : smm)
- {
- if (sm.getSequence() == seq)
- {
- continue;
- }
- }
+ selectedSequence = userSelectedSeq;
}
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
+ new SequenceI[] { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
- if (seq.getPrimaryDBRefs().size() == 0)
+ SwingUtilities.invokeLater(new Runnable()
{
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
}
- if (!seqsWithoutSourceDBRef.isEmpty())
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
+ {
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
{
- int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
- "status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
- SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
{
- seqWithoutSrcDBRef[x++] = fSeq;
+
}
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
- }
- }
- 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]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
}
/**
+ * Answers a structure viewer (new or existing) configured to superimpose
+ * added structures or not according to the user's choice
+ *
+ * @param ssm
+ * @return
+ */
+ StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
+ {
+ Object sv = targetView.getSelectedItem();
+
+ return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
+ }
+
+ /**
* 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)
+ protected void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq,
+ JLabel lbl_associateSeq)
{
cmb_assSeq.removeAllItems();
- cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
- null));
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", null));
lbl_associateSeq.setVisible(false);
if (selectedSequences.length > 1)
{
}
}
- public boolean isStructuresDiscovered()
+ protected boolean isStructuresDiscovered()
{
return discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty();
}
- public Collection<FTSData> getDiscoveredStructuresSet()
- {
- return discoveredStructuresSet;
- }
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
+ // this.
+ // Doing a search for "1" or "1c" is valuable?
+ // Those work but are enormously slow.
@Override
protected void txt_search_ActionPerformed()
{
- new Thread()
- {
- @Override
- public void run()
+ String text = txt_search.getText().trim();
+ if (text.length() >= PDB_ID_MIN)
+ new Thread()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
+
+ @Override
+ public void run()
{
- 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)
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (text.length() > 0)
{
- isValidPBDEntry = true;
+ // TODO move this pdb id search into the PDB specific
+ // FTSSearchEngine
+ // for moment, it will work fine as is because it is self-contained
+ String searchTerm = text.toLowerCase(Locale.ROOT);
+ 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);
+ FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
}
+ validateSelections();
}
- validateSelections();
- }
- }.start();
+ }.start();
}
@Override
- public void tabRefresh()
+ protected void tabRefresh()
{
if (selectedSequences != null)
{
+ lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
public void run()
{
fetchStructuresMetaData();
- filterResultSet(((FilterOption) cmb_filterOption
- .getSelectedItem()).getValue());
+ // populateFilterComboBox(true, cachedPDBExists);
+
+ filterResultSet(
+ ((FilterOption) cmb_filterOption.getSelectedItem())
+ .getValue());
+ lbl_loading.setVisible(false);
}
});
refreshThread.start();
public class PDBEntryTableModel extends AbstractTableModel
{
- String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
private List<CachedPDB> pdbEntries;
public PDBEntryTableModel(List<CachedPDB> pdbEntries)
{
- this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+ this.pdbEntries = new ArrayList<>(pdbEntries);
}
@Override
value = entry.getSequence();
break;
case 1:
- value = entry.getPdbEntry();
+ value = entry.getQualifiedId();
break;
case 2:
- value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
- .getPdbEntry().getChainCode();
+ value = entry.getPdbEntry().getChainCode() == null ? "_"
+ : entry.getPdbEntry().getChainCode();
break;
case 3:
value = entry.getPdbEntry().getType();
this.pdbEntry = pdbEntry;
}
+ public String getQualifiedId()
+ {
+ if (pdbEntry.hasProvider())
+ {
+ return pdbEntry.getProvider() + ":" + pdbEntry.getId();
+ }
+ return pdbEntry.toString();
+ }
+
public SequenceI getSequence()
{
return sequence;
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(long id, IProgressIndicatorHandler handler)
{
return progressBar.operationInProgress();
}
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
+
+ @Override
+ protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
+ {
+ data.setDocFieldPrefs(newPrefs);
+
+ }
+
+ /**
+ *
+ * @return true when all initialisation threads have finished and dialog is
+ * visible
+ */
+ public boolean isDialogVisible()
+ {
+ return mainFrame != null && data != null && cmb_filterOption != null
+ && mainFrame.isVisible()
+ && cmb_filterOption.getSelectedItem() != null;
+ }
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB()
+ {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}