package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
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.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
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.JTable;
+import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
/**
*
*/
@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser implements
- IProgressIndicator
+public class StructureChooser extends GStructureChooser
+ implements IProgressIndicator
{
- private boolean structuresDiscovered = false;
+ private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- private SequenceI selectedSequence;
+ private static final int MAX_QLENGTH = 7820;
- private SequenceI[] selectedSequences;
+ protected SequenceI selectedSequence;
+
+ public SequenceI[] selectedSequences;
private IProgressIndicator progressIndicator;
- private Collection<FTSData> discoveredStructuresSet;
+ protected Collection<FTSData> discoveredStructuresSet;
+
+ protected FTSRestRequest lastPdbRequest;
- private FTSRestRequest lastPdbRequest;
+ protected FTSRestClientI pdbRestClient;
- private FTSRestClientI pdbRestCleint;
+ protected String selectedPdbFileName;
- private String selectedPdbFileName;
+ protected boolean isValidPBDEntry;
- private boolean isValidPBDEntry;
+ protected boolean cachedPDBExists;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
/**
* 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));
+
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
.getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager
- .getString("status.searching_for_pdb_structures"),
- startTime);
+ updateProgressIndicator(MessageManager.getString(
+ "status.searching_for_pdb_structures"), startTime);
fetchStructuresMetaData();
- populateFilterComboBox();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ discoverStructureViews();
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
}
/**
+ * 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.
+ */
+ protected void discoverStructureViews()
+ {
+ Desktop desktop = Desktop.getInstance();
+ if (desktop != null)
+ {
+ targetView.removeAllItems();
+ if (desktop.lastTargetedView != null
+ && !desktop.lastTargetedView.isVisible())
+ {
+ desktop.lastTargetedView = null;
+ }
+ int linkedViewsAt = 0;
+ for (StructureViewerBase view : desktop
+ .getStructureViewers(null, null))
+ {
+ StructureViewer viewHandler = (desktop.lastTargetedView != null
+ && desktop.lastTargetedView.sview == view)
+ ? desktop.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 (desktop.lastTargetedView != null)
+ {
+ targetView.setSelectedItem(desktop.lastTargetedView);
+ }
+ else
+ {
+ targetView.setSelectedIndex(0);
+ }
+ }
+ btn_add.setVisible(targetView.isVisible());
+ }
+ }
+
+ /**
* Updates the progress indicator with the specified message
*
* @param message
* @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 = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> 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);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
{
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
}
}
}
-
+ cachedPDBExists = !entries.isEmpty();
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
tbl_local_pdb.setModel(tableModelx);
}
* @return the built query string
*/
- public static String buildQuery(SequenceI seq)
+ static String buildQuery(SequenceI seq)
{
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
+ queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
}
}
}
- if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
+ List<DBRefEntry> refs = seq.getDBRefs();
+ if (refs != null && refs.size() != 0)
{
- for (DBRefEntry dbRef : seq.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ DBRefEntry dbRef = refs.get(ib);
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- queryBuilder
-.append("uniprot_accession").append(":")
- .append(getDBRefId(dbRef))
- .append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
+ 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(":").append(getDBRefId(dbRef).toLowerCase())
- .append(" OR ");
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
isPDBRefsFound = true;
}
else
}
/**
- * Remove the following special characters from input string +, -, &, |, !, (,
- * ), {, }, [, ], ^, ", ~, *, ?, :, \
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
*
* @param seqName
* @return
*/
- private static String sanitizeSeqName(String seqName)
+ static String sanitizeSeqName(String seqName)
{
Objects.requireNonNull(seqName);
return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+");
+ .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)
+ static boolean isValidSeqName(String seqName)
{
// System.out.println("seqName : " + seqName);
String ignoreList = "pdb,uniprot,swiss-prot";
return true;
}
- public static String getDBRefId(DBRefEntry dbRef)
+ static String getDBRefId(DBRefEntry dbRef)
{
String ref = dbRef.getAccessionId().replaceAll("GO:", "");
return ref;
* @param fieldToFilterBy
* the field to filter by
*/
- public void filterResultSet(final String fieldToFilterBy)
+ void filterResultSet(final String fieldToFilterBy)
{
Thread filterThread = new Thread(new Runnable()
{
public void run()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
+ pdbRestClient = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
FTSRestRequest pdbRequest = new FTSRestRequest();
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
- System.out.println(">>>>>> Filtering with uniprot coverate");
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(");
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
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);
- tbl_summary.setModel(FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
-
- FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
- tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
- tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
- tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
+ 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);
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_filter_time", totalTime));
}
{
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"));
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)));
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- @Override
- protected void populateFilterComboBox()
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist)
{
- if (isStructuresDiscovered())
+ /*
+ * 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));
- cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
- "uniprot_coverage", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption(
+ 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("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));
+ 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);
}
/**
* Updates the displayed view based on the selected filter option
*/
- @Override
protected void updateCurrentView()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
}
/**
- * 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 (tbl_summary.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);
}
/**
* 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();
}
}
/**
- * 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
- public void ok_ActionPerformed()
+ protected void newView_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
- new Thread(new Runnable()
+ targetView.setSelectedItem(null);
+ showStructures(false);
+ }
+
+ /**
+ * Handles the 'Add to existing viewer' action
+ */
+ @Override
+ protected void add_ActionPerformed()
+ {
+ showStructures(false);
+ }
+
+ /**
+ * structure viewer opened by this dialog, or null
+ */
+ protected StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
+ final int preferredHeight = pnl_filter.getHeight();
+
+ Runnable viewStruc = new Runnable()
{
@Override
public void run()
{
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
- int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ 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 = restable.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
- .getModelIndex();
- int[] selectedRows = tbl_summary.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
- .toString();
- SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
+ .getModelIndex();
+ int[] selectedRows = restable.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ String pdbIdStr = restable
+ .getValueAt(row, pdbIdColIndex).toString();
+ SequenceI selectedSeq = (SequenceI) restable
+ .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);
+
+ 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()]);
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs);
}
- 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;
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
-
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
+ 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()]);
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
}
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
+ 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)
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
+ new SequenceI[]
+ { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = AssociatePdbFileWithSeq
+ .associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+
+ sViewer = launchStructureViewer(
+ ap, new PDBEntry[]
+ { fileEntry },
+ new SequenceI[]
+ { selectedSequence });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
+ }
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
{
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
{
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
+ {
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
- }
- mainFrame.dispose();
+ }
}
- }).start();
+ }
}
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ protected PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
Objects.requireNonNull(pdbEntries);
return foundEntry;
}
- private void launchStructureViewer(StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
+ /**
+ * Answers a structure viewer (new or existing) configured to superimpose
+ * added structures or not according to the user's choice
+ *
+ * @return
+ */
+ StructureViewer getTargetedStructureViewer()
{
- ssm.setProgressBar("Launching PDB structure viewer..");
- final StructureViewer sViewer = new StructureViewer(ssm);
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ Object sv = (targetView == null ? null : targetView.getSelectedItem());
- if (SiftsSettings.isMapWithSifts())
- {
- for (SequenceI seq : sequences)
- {
- if (seq.getSourceDBRef() == null)
- {
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching Database refs..");
- new jalview.ws.DBRefFetcher(sequences, null, null, null, false)
- .fetchDBRefs(true);
- break;
- }
- }
- }
- 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("Fetching PDB Structures for selected entries..");
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structure for "
- + pdbEntriesToView[0].getId());
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
+ return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
+ }
+
+ /**
+ * Adds PDB structures to a new or existing structure viewer
+ *
+ * @param ap
+ * @param pdbEntriesToView
+ * @param sequences
+ * @param superimpose
+ * @return viewer
+ */
+ protected StructureViewer launchStructureViewer(
+ AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
+ SequenceI[] selectedSeqs)
+ {
+ boolean superimpose = chk_superpose.isSelected();
+ /*
+ * remember user's choice of superimpose or not
+ */
+ Cache.setProperty(AUTOSUPERIMPOSE,
+ Boolean.valueOf(superimpose).toString());
+ return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
+ superimpose, getTargetedStructureViewer(), progressBar);
}
/**
* 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()
- {
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
+ protected boolean isStructuresDiscovered()
{
- this.structuresDiscovered = structuresDiscovered;
+ 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()
{
+ String text = txt_search.getText().trim();
+ if (text.length() >= PDB_ID_MIN)
+ {
new Thread()
{
- @Override
+
+ @Override
public void run()
{
errorWarning.setLength(0);
isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
+ if (text.length() > 0)
{
- String searchTerm = txt_search.getText().toLowerCase();
+ String searchTerm = text.toLowerCase();
searchTerm = searchTerm.split(":")[0];
- System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ // 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.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
errorWarning.append(e.getMessage());
}
}.start();
}
+ }
@Override
- public void tabRefresh()
+ protected void tabRefresh()
{
if (selectedSequences != null)
{
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" };
+ 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.getPdbEntry();
break;
case 2:
- value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
- .getPdbEntry().getChainCode();
+ value = entry.getPdbEntry().getChainCode() == null ? "_"
+ : entry.getPdbEntry().getChainCode();
break;
case 3:
value = entry.getPdbEntry().getType();
@Override
public void setProgressBar(String message, long id)
{
- progressBar.setProgressBar(message, id);
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(message, id);
+ }
}
@Override
{
return progressBar.operationInProgress();
}
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
}
git://source.jalview.org / jalview.git / blobdiff