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);
}
/**
* Updates the displayed view based on the selected filter option
*/
protected void updateCurrentView()
{
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);
// 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();
}
/**
* 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()
{
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();
}
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
*/
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);
}
}
/**
* 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-")))
{
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);
}
}
@Override
protected void cmbAssSeqStateChanged()
{
validateSelections();
}
private FilterOption lastSelected = null;
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
*/
@Override
protected void stateChanged(ItemEvent e)
{
if (e.getSource() instanceof JCheckBox)
{
updateCurrentView();
}
else
{
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;
}
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
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)
{
while (sViewer == null ? runner.isAlive()
: (sViewer.sview == null ? true
: !sViewer.sview.hasMapping()))
{
try
{
Thread.sleep(300);
} catch (InterruptedException ie)
{
}
}
}
}
/**
* 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)
{
lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
public void run()
{
fetchStructuresMetaData();
// 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" };
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;
}
}