/*
+
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
import java.util.List;
-import java.util.Vector;
import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
import javax.swing.JOptionPane;
-import javax.swing.ListSelectionModel;
+import javax.swing.table.DefaultTableModel;
+
/**
* Provides the behaviors for the Structure chooser Panel
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
- private PDBRestRequest pdbRequest;
+ private PDBRestRequest lastPdbRequest;
private PDBRestClient pdbRestCleint;
+ private String selectedPdbFileName;
+
+ private boolean isValidPBDEntry;
+
+ private static Hashtable<String, PDBEntry> cachedEntryMap;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
long startTime = System.currentTimeMillis();
String msg = MessageManager.getString("status.fetching_db_refs");
updateProgressIndicator(msg, startTime);
+ loadLocalCachedPDBEntries();
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- // wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- // wantedFields.add(PDBDocField.GENUS);
- // wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
- pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setWantedFields(wantedFields);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
+ }
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequenceDbRef(seq, resultList.getSearchSummary());
+ updateSequencePDBEntries(seq, resultList.getSearchSummary());
}
}
int noOfStructuresFound = 0;
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- jList_FoundStructures.setModel(PDBRestResponse
- .getListModel(discoveredStructuresSet));
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
- // resizeColumnWidth(summaryTable);
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ + " Found (" + totalTime + ")");
+ }
+ else
+ {
+ mainFrame
+.setTitle("Structure Chooser - Manual association");
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder();
+ // "Operation was unsucessful due to the following: \n");
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ }
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
- + " Found (" + totalTime + ")");
+ }
+
+ public void loadLocalCachedPDBEntries()
+ {
+ DefaultTableModel tableModel = new DefaultTableModel();
+ tableModel.addColumn("Sequence");
+ tableModel.addColumn("PDB Id");
+ tableModel.addColumn("Chain");
+ tableModel.addColumn("Type");
+ tableModel.addColumn("File");
+ cachedEntryMap = new Hashtable<String, PDBEntry>();
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.getDatasetSequence() != null
+ && seq.getDatasetSequence().getPDBId() != null)
+ {
+ for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+ {
+
+ String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
+ .getChainCode();
+ String[] pdbEntryRowData = new String[]
+ { seq.getDisplayId(false), pdbEntry.getId(),
+ chain,
+ pdbEntry.getType(),
+ pdbEntry.getFile() };
+ if (pdbEntry.getFile() != null)
+ {
+ tableModel.addRow(pdbEntryRowData);
+ }
+ cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
+ pdbEntry);
+ }
+ }
+ }
+ tbl_local_pdb.setModel(tableModel);
}
/**
- * Update the DBRef entry for a given sequence with values retrieved from
+ * Update the PDBEntry for a given sequence with values retrieved from
* PDBResponseSummary
*
* @param seq
* @param responseSummaries
* a collection of PDBResponseSummary
*/
- public void updateSequenceDbRef(SequenceI seq,
+ public void updateSequencePDBEntries(SequenceI seq,
Collection<PDBResponseSummary> responseSummaries)
{
for (PDBResponseSummary response : responseSummaries)
{
- PDBEntry newEntry = new PDBEntry();
- newEntry.setId(response.getPdbId());
- newEntry.setType("PDB");
- seq.getDatasetSequence().addPDBId(newEntry);
+ String pdbIdStr = response.getPdbId();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+ seq.getDatasetSequence().addPDBId(pdbEntry);
}
}
* the sequences to build a query for
* @return the built query string
*/
- @SuppressWarnings("unchecked")
+
public static String buildQuery(SequenceI seq)
{
- String query = seq.getName();
- StringBuilder queryBuilder = new StringBuilder();
- int count = 0;
+ HashSet<String> seqRefs = new LinkedHashSet<String>();
+ String seqName = seq.getName();
+ String[] names = seqName.toLowerCase().split("\\|");
+ for (String name : names)
+ {
+ // System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
+ {
+ seqRefs.add(name);
+ }
+ }
if (seq.getPDBId() != null)
{
- for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+ for (PDBEntry entry : seq.getPDBId())
{
- queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+ seqRefs.add(entry.getId());
}
}
if (seq.getDBRef() != null && seq.getDBRef().length != 0)
{
+ int count = 0;
for (DBRefEntry dbRef : seq.getDBRef())
{
- queryBuilder.append("text:")
- .append(dbRef.getAccessionId().replaceAll("GO:", ""))
- .append(" OR ");
+ seqRefs.add(getDBRefId(dbRef));
++count;
if (count > 10)
{
break;
}
}
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- query = queryBuilder.toString().substring(5, endIndex);
}
- // System.out.println("Query -----> " + query);
+
+ StringBuilder queryBuilder = new StringBuilder();
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ String query = queryBuilder.toString().substring(5, endIndex);
return query;
}
/**
+ * 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)
+ {
+ String ignoreList = "pdb,uniprot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.equalsIgnoreCase(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
@Override
public void run()
{
- try
+ long startTime = System.currentTimeMillis();
+ lbl_loading.setVisible(true);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
+ for (SequenceI seq : selectedSequences)
{
- lbl_loading.setVisible(true);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setFieldToSortBy(fieldToFilterBy,
!chk_invertFilter.isSelected());
-
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
{
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint
- .executeRequest(pdbRequest);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
}
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
- if (filteredResponse != null)
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
+
+ // Update table selection model here
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+ }
+ else
+ {
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+ if (errors.size() > 0)
{
- int filterResponseCount = filteredResponse.size();
- List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
- discoveredStructuresSet);
- originalDiscoveredStructuresList.removeAll(filteredResponse);
-
- Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
- reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
-
- jList_FoundStructures.setModel(PDBRestResponse
- .getListModel(reorderedStructuresSet));
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
- reorderedStructuresSet));
-
- // int[] filterIndice = new int[filterResponseCount];
- ListSelectionModel model = tbl_summary.getSelectionModel();
- model.clearSelection();
- for (int x = 0; x < filterResponseCount; x++)
+ StringBuilder errorMsg = new StringBuilder(
+ "Operation unsucessful due to the following: \n");
+ for (String error : errors)
{
- // filterIndice[x] = x;
- model.addSelectionInterval(x, x);
+ errorMsg.append(error).append("\n");
}
-
- // Discard unwanted objects to make them eligible for garbage
- // collection
- originalDiscoveredStructuresList = null;
- reorderedStructuresSet = null;
-
- // jListFoundStructures.setSelectedIndices(filterIndice);
+ JOptionPane.showMessageDialog(null, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
}
-
- lbl_loading.setVisible(false);
- } catch (Exception e)
- {
- e.printStackTrace();
}
+
+ lbl_loading.setVisible(false);
+
+ validateSelections();
}
});
filterThread.start();
}
- /**
- * Determines the column index for the pdb id in the summary table. The pdb id
- * serves as a unique identifier for a given row in the summary table
- *
- * @param wantedFeilds
- * the available table columns in no particular order
- * @return the pdb id field column index
- */
- public static int getPDBIdColumIndex(Collection<PDBDocField> wantedFeilds)
- {
- int pdbFeildIndex = 1;
- for (PDBDocField feild : wantedFeilds)
- {
- if (feild.equals(PDBDocField.PDB_ID))
- {
- break;
- }
- ++pdbFeildIndex;
- }
- return pdbFeildIndex;
- }
/**
* Handles action event for btn_pdbFromFile
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, selectedSequence, true,
- Desktop.instance);
- }
- }
-
- /**
- * Handles action event for btn_ok
- */
- @Override
- public void ok_ActionPerformed()
- {
- int pdbIdCol = getPDBIdColumIndex(pdbRequest.getWantedFields());
- int[] selectedRows = tbl_summary.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- for (int summaryRow : selectedRows)
- {
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType("PDB");
- pdbEntriesToView[count++] = pdbEntry;
- }
- new StructureViewer(ap.getStructureSelectionManager()).viewStructures(
- ap, pdbEntriesToView, ap.av.collateForPDB(pdbEntriesToView));
- }
-
- /**
- * Handles action event for manual entry of pdb ids
- */
- public void enterPDB_actionPerformed()
- {
- 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)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- selectedSequence.getDatasetSequence().addPDBId(entry);
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
}
}
VIEWS_ENTER_ID));
cmb_filterOption.addItem(new FilterOption("From File", "-",
VIEWS_FROM_FILE));
+ cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
+ VIEWS_LOCAL_PDB));
}
/**
*/
protected void updateCurrentView()
{
- FilterOption selectedOption = ((FilterOption) cmb_filterOption
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
layout_switchableViews.show(pnl_switchableViews,
- selectedOption.getView());
- chk_invertFilter.setEnabled(false);
- if (selectedOption.getView() == VIEWS_FILTER)
+ 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(filterTitle);
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
+ }
+
+ /**
+ * Validates user selection and activates the view button if all parameters
+ * are correct
+ */
+ public void validateSelections()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ if (tbl_summary.getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
{
- chk_invertFilter.setEnabled(true);
- filterResultSet(selectedOption.getValue());
+ 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, "No PDB entry found for \'" + txt_search.getText()
+ + "\'"));
+ }
+
+ if (errorWarning.length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setIcon(warningImage);
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+ true, errorWarning.toString()));
+ }
+
+ if (selectedSequences.length == 1
+ || !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
+ }
+
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ public void validateAssociationFromFile()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_fromFileStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null
+ && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ {
+ btn_view.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
+ }
+ }
+
+ @Override
+ public void cmbAssSeqStateChanged()
+ {
+ validateSelections();
+ }
+
+ /**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
*/
}
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
+ lastPdbRequest.getWantedFields(), true);
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ pdbEntriesToView, ap, selectedSequences);
+ }
+ else if(currentView == VIEWS_LOCAL_PDB){
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int row : selectedRows)
+ {
+ String entryKey = tbl_local_pdb.getValueAt(row, 1).toString()
+ .toLowerCase();
+ pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+ }
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ pdbEntriesToView, ap, selectedSequences);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ PDBEntry[] pdbEntriesToView = new PDBEntry[]
+ { pdbEntry };
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ pdbEntriesToView, ap, new SequenceI[]
+ { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(
+ selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
+
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ new PDBEntry[]
+ { fileEntry }, ap, new SequenceI[]
+ { selectedSequence });
+ }
+ mainFrame.dispose();
+ }
+
+ private void launchStructureViewer(StructureSelectionManager ssm,
+ PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
+ SequenceI[] selectedSequences)
+ {
+ StructureViewer sViewer = new StructureViewer(ssm);
+ if (pdbEntriesToView.length > 1)
+ {
+ sViewer.viewStructures(alignPanel, pdbEntriesToView,
+ alignPanel.av.collateForPDB(pdbEntriesToView));
+ }
+ else
+ {
+ sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+ alignPanel);
+ }
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ public 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("Auto Detect", null));
+ lbl_associateSeq.setVisible(false);
+ if (selectedSequences.length > 1)
+ {
+ for (SequenceI seq : selectedSequences)
+ {
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+ }
+ }
+ else
+ {
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
+ cmb_assSeq.setVisible(false);
+ }
+ }
public boolean isStructuresDiscovered()
{
{
return discoveredStructuresSet;
}
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ // JOptionPane.showMessageDialog(this, e.getMessage(),
+ // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ // System.out.println(">>>>> executing finally block");
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
+ validateSelections();
+ }
+
+ @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();
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff