/*
- * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.phyre2.Phyre2Client;
+import jalview.ws.phyre2.Phyre2SummaryPojo;
import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.table.AbstractTableModel;
/**
public class StructureChooser extends GStructureChooser implements
IProgressIndicator
{
+ private static int MAX_QLENGTH = 7820;
+
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private FTSRestClientI pdbRestCleint;
- private String selectedPdbFileName;
+ private String selectedStructureFileName;
private boolean isValidPBDEntry;
&& !discoveredStructuresSet.isEmpty())
{
getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
+ JvSummaryTable.getTableModel(lastPdbRequest,
discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
{
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);
}
}
}
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<String>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
queryBuilder.append("pdb_id:")
.append(entry.getId().toLowerCase()).append(" OR ");
isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
}
}
}
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
+ JvSummaryTable.getTableModel(lastPdbRequest,
reorderedStructuresSet));
- FTSRestResponse.configureTableColumn(getResultTable(),
+ JvSummaryTable.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
getResultTable().getColumn("Ref Sequence").setMinWidth(100);
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
+ JvOptionPane.showMessageDialog(
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ selectedStructureFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedStructureFileName);
validateSelections();
}
}
if (haveData)
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
- "overall_quality", VIEWS_FILTER));
+ "overall_quality", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
+ "resolution", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
+ "number_of_protein_chains", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
+ "number_of_bound_molecules", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
+ "number_of_polymer_residues", VIEWS_FILTER, true));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
+ VIEWS_ENTER_ID, false));
cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB);
- cmb_filterOption.addItem(cachedOption);
+ VIEWS_FROM_FILE, false));
- if (/*!haveData &&*/cachedPDBExists)
+ if (cachedPDBExists)
{
+ FilterOption cachedOption = new FilterOption("Cached PDB Entries",
+ "-", VIEWS_LOCAL_PDB, false);
+ cmb_filterOption.addItem(cachedOption);
cmb_filterOption.setSelectedItem(cachedOption);
}
+ cmb_filterOption.addItem(new FilterOption(
+ "Predict 3D Model with Phyre2", "-", VIEWS_PHYRE2_PREDICTION,
+ false));
cmb_filterOption.addItemListener(this);
}
chk_invertFilter.setVisible(true);
filterResultSet(selectedFilterOpt.getValue());
}
+ else if (selectedFilterOpt.getView() == VIEWS_PHYRE2_PREDICTION)
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.phyre2_model_prediction"));
+ phyre2InputAssSeqPanel.loadCmbAssSeq();
+ }
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
{
validateAssociationFromFile();
}
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
+ {
+ validateAssociationFromPhyre2();
+ if (getPhyreResultTable().getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
}
/**
"-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
- if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ if (selectedStructureFileName != null && selectedStructureFileName.length() > 0)
{
btn_view.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
+ /**
+ * Validates inputs for Phyre2 3D Model prediction
+ */
+ public void validateAssociationFromPhyre2()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) phyre2InputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_runPhyre2Prediction.setEnabled(true);
+ }
+ else
+ {
+ btn_runPhyre2Prediction.setEnabled(false);
+ }
+ }
+
@Override
public void cmbAssSeqStateChanged()
{
@Override
public void ok_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
+ ssm.setMappingForPhyre2Model(false);
new Thread(new Runnable()
{
@Override
int[] selectedRows = getResultTable().getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
String pdbIdStr = getResultTable().getValueAt(row,
.getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
selectedSequence = userSelectedSeq;
}
+
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(selectedStructureFileName,
+ DataSourceType.FILE,
+ selectedSequence, true, Desktop.instance);
+
+ launchStructureViewer(ssm,
+ new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[] { selectedSequence });
}
- else if (currentView == VIEWS_FROM_FILE)
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
{
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) phyre2InputAssSeqPanel
.getCmb_assSeq().getSelectedItem()).getSequence();
if (userSelectedSeq != null)
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ int templateColIndex = getPhyreResultTable()
+ .getColumn("Template")
+ .getModelIndex();
+ int[] selectedRows = getPhyreResultTable().getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int row : selectedRows)
+ {
+ String templateId = getPhyreResultTable().getValueAt(row,
+ templateColIndex).toString();
+ String structureFile = phyre2ResultDirectory + templateId
+ + ".pdb";
+ pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(structureFile,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+ }
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
+ final StructureSelectionManager ssm = ap
+ .getStructureSelectionManager();
+ ssm.setMappingForPhyre2Model(true);
+ final long progressSessionId = System.currentTimeMillis();
+ ssm.setProgressSessionId(progressSessionId);
+
+ SequenceI[] sequences = new SequenceI[] { selectedSequence };
+
+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
+ final StructureViewer sViewer = new StructureViewer(ssm);
+ if (pdbEntriesToView.length > 1)
+ {
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ for (SequenceI seq : sequences)
+ {
+ seqsMap.add(new SequenceI[] { seq });
+ }
+ SequenceI[][] collatedSeqs = seqsMap
+ .toArray(new SequenceI[0][0]);
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"));
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs, ap);
+ }
+ else
+ {
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()));
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+ }
}
closeAction(preferredHeight);
}
}).start();
}
+ private String phyre2ResultDirectory;
+
+ @Override
+ public void predict3DModelWithPhyre2()
+ {
+ // TODO implement code for submitting sequence to Phyre2 service, and code
+ // for getting the result directory when the job completes, this is
+ // currently hard-wired to the directory of result for FER_CAPAN/1-144
+ phyre2ResultDirectory = "examples/testdata/phyre2results/56da5616b4559c93/";
+ String summaryhtml = phyre2ResultDirectory + "summary.html";
+ // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for
+ // Phyre2 result summary is made available
+ List<Phyre2SummaryPojo> phyreResults = Phyre2Client
+ .parsePhyre2ResultSummaryTable(summaryhtml);
+ getPhyreResultTable()
+ .setModel(Phyre2Client.getTableModel(phyreResults));
+ Phyre2Client.configurePhyreResultTable(getPhyreResultTable());
+ }
+
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
final StructureViewer sViewer = new StructureViewer(ssm);
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
// 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 (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ y), progressId);
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
seqWithoutSrcDBRef[x++] = fSeq;
}
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
+ new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ setProgressBar("Fetch complete.", progressId); // todo i18n
}
}
if (pdbEntriesToView.length > 1)
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
+ setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
}
/**
git://source.jalview.org / jalview.git / blobdiff