X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=358412d81f5efeb19e3ec00262245533c009ba1b;hb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;hp=f28ef68fbe84a9edf53015b80d0d4da36c4a6061;hpb=fd235cc7542d6e308e054a8a76580a6c511ae631;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index f28ef68..358412d 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,4 +1,5 @@ /* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors * @@ -26,6 +27,7 @@ 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; @@ -37,12 +39,15 @@ import java.awt.event.ItemEvent; 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.ListSelectionModel; +import javax.swing.JLabel; +import javax.swing.table.DefaultTableModel; + /** * Provides the behaviors for the Structure chooser Panel @@ -61,9 +66,9 @@ public class StructureChooser extends GStructureChooser private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet = new HashSet(); + private Collection discoveredStructuresSet; - private PDBRestRequest pdbRequest; + private PDBRestRequest lastPdbRequest; private PDBRestClient pdbRestCleint; @@ -71,6 +76,8 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; + private static Hashtable cachedEntryMap; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -94,6 +101,7 @@ public class StructureChooser extends GStructureChooser long startTime = System.currentTimeMillis(); String msg = MessageManager.getString("status.fetching_db_refs"); updateProgressIndicator(msg, startTime); + loadLocalCachedPDBEntries(); fetchStructuresMetaData(); populateFilterComboBox(); updateProgressIndicator(null, startTime); @@ -130,17 +138,19 @@ public class StructureChooser extends GStructureChooser Collection wantedFields = PDBDocFieldPreferences .getStructureSummaryFields(); - pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setWantedFields(wantedFields); + discoveredStructuresSet = new LinkedHashSet(); 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); + lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { @@ -153,7 +163,7 @@ public class StructureChooser extends GStructureChooser if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest, + tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); @@ -164,6 +174,38 @@ public class StructureChooser extends GStructureChooser + " 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(); + 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() }; + tableModel.addRow(pdbEntryRowData); + cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(), + pdbEntry); + } + } + } + tbl_local_pdb.setModel(tableModel); + } + /** * Update the DBRef entry for a given sequence with values retrieved from * PDBResponseSummary @@ -180,7 +222,7 @@ public class StructureChooser extends GStructureChooser { PDBEntry newEntry = new PDBEntry(); newEntry.setId(response.getPdbId()); - newEntry.setType("PDB"); + newEntry.setType(PDBEntry.Type.PDB); seq.getDatasetSequence().addPDBId(newEntry); } } @@ -192,41 +234,85 @@ public class StructureChooser extends GStructureChooser * 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 seqRefs = new LinkedHashSet(); + 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) 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); } + + 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 @@ -243,19 +329,25 @@ public class StructureChooser extends GStructureChooser try { lbl_loading.setVisible(true); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); + Collection wantedFields = PDBDocFieldPreferences + .getStructureSummaryFields(); Collection filteredResponse = new HashSet(); for (SequenceI seq : selectedSequences) { + PDBRestRequest pdbRequest = new PDBRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(text:"); + pdbRequest.setFieldToSortBy(fieldToFilterBy, + !chk_invertFilter.isSelected()); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); + pdbRequest.setWantedFields(wantedFields); pdbRequest.setAssociatedSequence(seq.getName()); pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList = pdbRestCleint .executeRequest(pdbRequest); + lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { @@ -263,50 +355,37 @@ public class StructureChooser extends GStructureChooser } } - if (filteredResponse != null) + if (!filteredResponse.isEmpty()) { - int filterResponseCount = filteredResponse.size(); - List originalDiscoveredStructuresList = new ArrayList( - discoveredStructuresSet); - originalDiscoveredStructuresList.removeAll(filteredResponse); - Collection reorderedStructuresSet = new ArrayList(); + final int filterResponseCount = filteredResponse.size(); + Collection reorderedStructuresSet = new LinkedHashSet(); reorderedStructuresSet.addAll(filteredResponse); - reorderedStructuresSet.addAll(originalDiscoveredStructuresList); + reorderedStructuresSet.addAll(discoveredStructuresSet); + tbl_summary.setModel(PDBRestResponse.getTableModel( + lastPdbRequest, reorderedStructuresSet)); - tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest, - reorderedStructuresSet)); + // Update table selection model here + tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - ListSelectionModel model = tbl_summary.getSelectionModel(); - model.clearSelection(); - for (int x = 0; x < filterResponseCount; x++) - { - model.addSelectionInterval(x, x); - } - - // Discard unwanted objects to make them eligible for garbage - // collection - originalDiscoveredStructuresList = null; - reorderedStructuresSet = null; } lbl_loading.setVisible(false); + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; + mainFrame.setTitle("Structure Chooser - Filter time (" + + totalTime + ")"); + + validateSelections(); } catch (Exception e) { e.printStackTrace(); } - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime - + ")"); - - validateSelections(); } }); filterThread.start(); } - /** * Handles action event for btn_pdbFromFile */ @@ -356,6 +435,8 @@ public class StructureChooser extends GStructureChooser VIEWS_ENTER_ID)); cmb_filterOption.addItem(new FilterOption("From File", "-", VIEWS_FROM_FILE)); + cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", + VIEWS_LOCAL_PDB)); } /** @@ -376,7 +457,8 @@ public class StructureChooser extends GStructureChooser chk_invertFilter.setVisible(true); filterResultSet(selectedFilterOpt.getValue()); } - else + else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID + || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); @@ -401,6 +483,13 @@ public class StructureChooser extends GStructureChooser btn_view.setEnabled(true); } } + else if (currentView == VIEWS_LOCAL_PDB) + { + if (tbl_local_pdb.getSelectedRows().length > 0) + { + btn_view.setEnabled(true); + } + } else if (currentView == VIEWS_ENTER_ID) { validateAssociationEnterPdb(); @@ -409,7 +498,6 @@ public class StructureChooser extends GStructureChooser { validateAssociationFromFile(); } - } /** @@ -504,7 +592,7 @@ public class StructureChooser extends GStructureChooser if (currentView == VIEWS_FILTER) { int pdbIdCol = PDBRestClient.getPDBIdColumIndex( - pdbRequest.getWantedFields(), true); + lastPdbRequest.getWantedFields(), true); int[] selectedRows = tbl_summary.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; @@ -514,49 +602,93 @@ public class StructureChooser extends GStructureChooser .toString(); PDBEntry pdbEntry = new PDBEntry(); pdbEntry.setId(pdbIdStr); - pdbEntry.setType("PDB"); + pdbEntry.setType(PDBEntry.Type.PDB); pdbEntriesToView[count++] = pdbEntry; } - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pdbEntriesToView, - ap.av.collateForPDB(pdbEntriesToView)); + + 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, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString(); + pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); + } + launchStructureViewer(ap.getStructureSelectionManager(), + pdbEntriesToView, ap, selectedSequences); } else if (currentView == VIEWS_ENTER_ID) { - selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } PDBEntry pdbEntry = new PDBEntry(); pdbEntry.setId(txt_search.getText()); - pdbEntry.setType("PDB"); + pdbEntry.setType(PDBEntry.Type.PDB); selectedSequence.getDatasetSequence().addPDBId(pdbEntry); PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pdbEntriesToView, - ap.av.collateForPDB(pdbEntriesToView)); + launchStructureViewer(ap.getStructureSelectionManager(), + pdbEntriesToView, ap, new SequenceI[] + { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { - selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem()).getSequence(); - new AssociatePdbFileWithSeq().associatePdbWithSeq( + 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 cmb_assSeq) + JComboBox 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) @@ -566,6 +698,10 @@ public class StructureChooser extends GStructureChooser } 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); } } @@ -593,7 +729,7 @@ public class StructureChooser extends GStructureChooser { List wantedFields = new ArrayList(); wantedFields.add(PDBDocField.PDB_ID); - pdbRequest = new PDBRestRequest(); + PDBRestRequest pdbRequest = new PDBRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("(pdb_id:"); @@ -611,4 +747,23 @@ public class StructureChooser extends GStructureChooser 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(); + } + } + }