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(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)
+ {
+ 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);
}
- int debounceCount = 0;
+ /**
+ * Updates the displayed view based on the selected filter option
+ */
protected void updateCurrentView()
{
- FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
- switchableViewsLayout.show(switchableViewsPanel,
- currentOption.getView());
- ++debounceCount;
- if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0)
+
+ if (lastSelected == selectedFilterOpt)
{
- filterResultSet(currentOption.getValue());
+ // 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);
+ // 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)
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.structure_chooser_manual_association"));
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
}
- public void filterResultSet(String filterTarget)
+ /**
+ * 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.
+ *
+ * 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
+ protected void validateSelections()
{
- System.out.println("-----------------> Filter by : " + filterTarget);
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_add.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ int selectedCount = 0;
+ if (currentView == VIEWS_FILTER)
+ {
+ selectedCount = getResultTable().getSelectedRows().length;
+ if (selectedCount > 0)
+ {
+ btn_add.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ selectedCount = tbl_local_pdb.getSelectedRows().length;
+ if (selectedCount > 0)
+ {
+ btn_add.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ validateAssociationEnterPdb();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
+ }
- List wantedFields = new ArrayList();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
+ btn_newView.setEnabled(btn_add.isEnabled());
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(1);
- request.setSearchTarget("(text:");
- request.setSortTarget(filterTarget, true);
+ /*
+ * 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);
+ }
- request.setWantedFields(wantedFields);
+ @Override
+ protected boolean showPopupFor(int selectedRow, int x, int y)
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
- Collection searchSummaries = new HashSet();
- for (SequenceI seq : selectedSequences)
+ if (currentView == VIEWS_FILTER
+ && data instanceof ThreeDBStructureChooserQuerySource)
{
- request.setSearchTerm(buildQuery(seq) + ")");
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
+
+ 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()
{
- searchSummaries.addAll(resultList.getSearchSummary());
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ });
+ popup.add(viewUrl);
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ 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
+ */
+ protected void validateAssociationEnterPdb()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ if (txt_search.getText().length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("info.no_pdb_entry_found_for",
+ txt_search.getText())));
+ }
+ if (errorWarning.length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setIcon(warningImage);
+ lbl_pdbManualFetchStatus.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
+ }
+
+ if (selectedSequences.length == 1 || !assSeqOpt.getName()
+ .equalsIgnoreCase("-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_add.setEnabled(true);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
}
}
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
+ }
- for (PDBResponseSummary summary : searchSummaries)
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ 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-")))
{
- jListFoundStructures.setSelectedValue(summary, true);
- // jListFoundStructures.
- break;
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ {
+ btn_add.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
}
- System.out.println("Found item count : " + searchSummaries.size());
}
- public void pdbFromFile_actionPerformed()
+ @Override
+ protected void cmbAssSeqStateChanged()
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
- { selectedSequence.getDisplayId(false) }));
- chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
- { selectedSequence.getDisplayId(false) }));
+ validateSelections();
+ }
- int value = chooser.showOpenDialog(null);
+ private FilterOption lastSelected = null;
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ /**
+ * Handles the state change event for the 'filter' combo-box and 'invert'
+ * check-box
+ */
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
- Desktop.instance);
+ updateCurrentView();
+ }
+ else
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
}
}
+ /**
+ * 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;
+ }
- // rpdbview.addActionListener(new ActionListener()
- // {
- //
- // @Override
- // public void actionPerformed(ActionEvent e)
- // {
- // new StructureViewer(ap.getStructureSelectionManager())
- // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- // }
- // });
+ 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;
+ }
- public void enterPDB_actionPerformed()
+ /**
+ * Handles the 'New View' action
+ */
+ @Override
+ protected void newView_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)
+ 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
+ */
+ private StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
+ final int preferredHeight = pnl_filter.getHeight();
+
+ 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[] selectedRows = restable.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ List selectedSeqsToView = new ArrayList<>();
+ pdbEntriesToView = data.collectSelectedRows(restable,
+ selectedRows, selectedSeqsToView);
+
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
+ .getModelIndex();
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ List selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+ .getModel()).getPDBEntryAt(row).getPdbEntry();
+
+ 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(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ if (pdbIdStr.split(":").length > 1)
+ {
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(
+ pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
+
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ sViewer = 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);
+
+ sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+ ap, new SequenceI[]
+ { selectedSequence });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
+ }
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
{
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- selectedSequence.getDatasetSequence().addPDBId(entry);
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
+ {
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
+ {
+
+ }
+ }
}
}
- // public static void main(String[] args)
- // {
- // SwingUtilities.invokeLater(new Runnable()
- // {
- // public void run()
- // {
- // new StructureChooser(null, null);
- // }
- // });
- // }
+ /**
+ * 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;
+ }
+
+ /**
+ * Adds PDB structures to a new or existing structure viewer
+ *
+ * @param ssm
+ * @param pdbEntriesToView
+ * @param alignPanel
+ * @param sequences
+ * @return
+ */
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
+ {
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
+ final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+ boolean superimpose = chk_superpose.isSelected();
+ theViewer.setSuperpose(superimpose);
+ /*
+ * remember user's choice of superimpose or not
+ */
+ Cache.setProperty(AUTOSUPERIMPOSE,
+ Boolean.valueOf(superimpose).toString());
+ setProgressBar(null, progressId);
+ if (SiftsSettings.isMapWithSifts())
+ {
+ List seqsWithoutSourceDBRef = new ArrayList<>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+ for (SequenceI seq : sequences)
+ {
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
+ {
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (seq.getPrimaryDBRefs().isEmpty())
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y), progressId);
+ SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
+ if (pdbEntriesToView.length > 1)
+ {
+ setProgressBar(
+ MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ }
+ else
+ {
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()), progressId);
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
+ setProgressBar(null, progressId);
+ // remember the last viewer we used...
+ lastTargetedView = theViewer;
+ return theViewer;
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ @Override
+ protected void populateCmbAssociateSeqOptions(
+ JComboBox cmb_assSeq,
+ JLabel lbl_associateSeq)
+ {
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", 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);
+ }
+ }
+
+ protected boolean isStructuresDiscovered()
+ {
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
+ }
+
+ 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
+ public void run()
+ {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (text.length() > 0)
+ {
+ // 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 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();
+ }
+ }.start();
+ }
+
+ @Override
+ protected void tabRefresh()
+ {
+ if (selectedSequences != null)
+ {
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ // populateFilterComboBox(true, cachedPDBExists);
+
+ filterResultSet(
+ ((FilterOption) cmb_filterOption.getSelectedItem())
+ .getValue());
+ }
+ });
+ refreshThread.start();
+ }
+ }
+
+ public class PDBEntryTableModel extends AbstractTableModel
+ {
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
+
+ private List pdbEntries;
+
+ public PDBEntryTableModel(List pdbEntries)
+ {
+ this.pdbEntries = new ArrayList<>(pdbEntries);
+ }
+
+ @Override
+ public String getColumnName(int columnIndex)
+ {
+ return columns[columnIndex];
+ }
+
+ @Override
+ public int getRowCount()
+ {
+ return pdbEntries.size();
+ }
+
+ @Override
+ public int getColumnCount()
+ {
+ return columns.length;
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public Object getValueAt(int rowIndex, int columnIndex)
+ {
+ Object value = "??";
+ CachedPDB entry = pdbEntries.get(rowIndex);
+ switch (columnIndex)
+ {
+ case 0:
+ value = entry.getSequence();
+ break;
+ case 1:
+ value = entry.getQualifiedId();
+ break;
+ case 2:
+ value = entry.getPdbEntry().getChainCode() == null ? "_"
+ : entry.getPdbEntry().getChainCode();
+ break;
+ case 3:
+ value = entry.getPdbEntry().getType();
+ break;
+ case 4:
+ value = entry.getPdbEntry().getFile();
+ break;
+ }
+ return value;
+ }
+
+ @Override
+ public Class getColumnClass(int columnIndex)
+ {
+ return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
+ }
+
+ public CachedPDB getPDBEntryAt(int row)
+ {
+ return pdbEntries.get(row);
+ }
+
+ }
+
+ private class CachedPDB
+ {
+ private SequenceI sequence;
+
+ private PDBEntry pdbEntry;
+
+ public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
+ {
+ this.sequence = sequence;
+ this.pdbEntry = pdbEntry;
+ }
+
+ public String getQualifiedId()
+ {
+ if (pdbEntry.hasProvider())
+ {
+ return pdbEntry.getProvider() + ":" + pdbEntry.getId();
+ }
+ return pdbEntry.toString();
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public PDBEntry getPdbEntry()
+ {
+ return pdbEntry;
+ }
+
+ }
+
+ private IProgressIndicator progressBar;
+
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+
+ @Override
+ public void registerHandler(long id, IProgressIndicatorHandler handler)
+ {
+ progressBar.registerHandler(id, handler);
+ }
+
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar.operationInProgress();
+ }
+
+ 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;
+ }
}