X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3350f6cc62327c338415713360233537290d1a83;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=d924e735e916834f9144c4f1d96160893f7b014c;hpb=007af0c9001900071f6d8e9214143f79e10f4938;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index d924e73..3350f6c 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -33,8 +33,10 @@ import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.jbgui.GStructureChooser; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.ws.DBRefFetcher; import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; @@ -44,6 +46,7 @@ import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; import java.util.Objects; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBox; @@ -62,8 +65,6 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private boolean structuresDiscovered = false; - private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -80,6 +81,8 @@ public class StructureChooser extends GStructureChooser implements private boolean isValidPBDEntry; + private boolean cachedPDBExists; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -100,6 +103,8 @@ public class StructureChooser extends GStructureChooser implements progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + // ensure a filter option is in force for search + populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -114,7 +119,8 @@ public class StructureChooser extends GStructureChooser implements .getString("status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); - populateFilterComboBox(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -147,8 +153,8 @@ public class StructureChooser extends GStructureChooser implements { long startTime = System.currentTimeMillis(); pdbRestCleint = PDBFTSRestClient.getInstance(); - Collection wantedFields = pdbRestCleint - .getAllDefaulDisplayedDataColumns(); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); discoveredStructuresSet = new LinkedHashSet(); HashSet errors = new HashSet(); @@ -158,6 +164,10 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(500); pdbRequest.setFieldToSearchBy("("); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), + !chk_invertFilter.isSelected()); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); @@ -185,9 +195,9 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; + getResultTable().setModel( + FTSRestResponse.getTableModel(lastPdbRequest, + discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -229,7 +239,7 @@ public class StructureChooser extends GStructureChooser implements } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -247,7 +257,7 @@ public class StructureChooser extends GStructureChooser implements boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - HashSet seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet(); if (seq.getAllPDBEntries() != null) { @@ -255,10 +265,8 @@ public class StructureChooser extends GStructureChooser implements { if (isValidSeqName(entry.getId())) { - queryBuilder.append("pdb_id") - .append(":") -.append(entry.getId().toLowerCase()) - .append(" OR "); + queryBuilder.append("pdb_id:") + .append(entry.getId().toLowerCase()).append(" OR "); isPDBRefsFound = true; // seqRefs.add(entry.getId()); } @@ -273,22 +281,17 @@ public class StructureChooser extends GStructureChooser implements { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { - queryBuilder -.append("uniprot_accession").append(":") - .append(getDBRefId(dbRef)) - .append(" OR "); - queryBuilder -.append("uniprot_id") - .append(":") + queryBuilder.append("uniprot_accession:") .append(getDBRefId(dbRef)).append(" OR "); + queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) + .append(" OR "); isUniProtRefsFound = true; } else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append("pdb_id") - .append(":").append(getDBRefId(dbRef).toLowerCase()) - .append(" OR "); + queryBuilder.append("pdb_id:") + .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); isPDBRefsFound = true; } else @@ -330,20 +333,19 @@ public class StructureChooser extends GStructureChooser implements } /** - * Remove the following special characters from input string +, -, &, |, !, (, - * ), {, }, [, ], ^, ", ~, *, ?, :, \ + * Remove the following special characters from input string +, -, &, !, (, ), + * {, }, [, ], ^, ", ~, *, ?, :, \ * * @param seqName * @return */ - private static String sanitizeSeqName(String seqName) + static String sanitizeSeqName(String seqName) { Objects.requireNonNull(seqName); return seqName.replaceAll("\\[\\d*\\]", "") - .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+"); + .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); } - /** * Ensures sequence ref names are not less than 3 characters and does not * contain a database name @@ -396,8 +398,8 @@ public class StructureChooser extends GStructureChooser implements long startTime = System.currentTimeMillis(); pdbRestCleint = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); - Collection wantedFields = pdbRestCleint - .getAllDefaulDisplayedDataColumns(); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); @@ -406,7 +408,6 @@ public class StructureChooser extends GStructureChooser implements FTSRestRequest pdbRequest = new FTSRestRequest(); if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { - System.out.println(">>>>>> Filtering with uniprot coverate"); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("("); @@ -454,15 +455,18 @@ public class StructureChooser extends GStructureChooser implements Collection reorderedStructuresSet = new LinkedHashSet(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - tbl_summary.setModel(FTSRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); - - FTSRestResponse.configureTableColumn(tbl_summary, wantedFields); - tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120); - tbl_summary.getColumn("Ref Sequence").setMinWidth(100); - tbl_summary.getColumn("Ref Sequence").setMaxWidth(200); + getResultTable().setModel( + FTSRestResponse.getTableModel(lastPdbRequest, + reorderedStructuresSet)); + + FTSRestResponse.configureTableColumn(getResultTable(), + wantedFields, tempUserPrefs); + getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); + getResultTable().getColumn("Ref Sequence").setMinWidth(100); + getResultTable().getColumn("Ref Sequence").setMaxWidth(200); // Update table selection model here - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); + getResultTable().addRowSelectionInterval(0, + filterResponseCount - 1); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_filter_time", totalTime)); } @@ -522,15 +526,19 @@ public class StructureChooser extends GStructureChooser implements * Populates the filter combo-box options dynamically depending on discovered * structures */ - @Override - protected void populateFilterComboBox() + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExists) { - if (isStructuresDiscovered()) + /* + * temporarily suspend the change listener behaviour + */ + cmb_filterOption.removeItemListener(this); + + cmb_filterOption.removeAllItems(); + if (haveData) { cmb_filterOption.addItem(new FilterOption("Best Quality", "overall_quality", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage", - "uniprot_coverage", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Best Resolution", "resolution", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", @@ -544,14 +552,21 @@ public class StructureChooser extends GStructureChooser implements VIEWS_ENTER_ID)); cmb_filterOption.addItem(new FilterOption("From File", "-", VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-", + VIEWS_LOCAL_PDB); + cmb_filterOption.addItem(cachedOption); + + if (/*!haveData &&*/cachedPDBExists) + { + cmb_filterOption.setSelectedItem(cachedOption); + } + + cmb_filterOption.addItemListener(this); } /** * Updates the displayed view based on the selected filter option */ - @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -591,7 +606,7 @@ public class StructureChooser extends GStructureChooser implements String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - if (tbl_summary.getSelectedRows().length > 0) + if (getResultTable().getSelectedRows().length > 0) { btn_view.setEnabled(true); } @@ -717,6 +732,7 @@ public class StructureChooser extends GStructureChooser implements { final long progressSessionId = System.currentTimeMillis(); final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); ssm.setProgressIndicator(this); ssm.setProgressSessionId(progressSessionId); new Thread(new Runnable() @@ -724,108 +740,116 @@ public class StructureChooser extends GStructureChooser implements @Override public void run() { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) - { - int pdbIdColIndex = tbl_summary.getColumn("PDB Id") + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER) + { + int pdbIdColIndex = getResultTable().getColumn("PDB Id") .getModelIndex(); - int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") - .getModelIndex(); - int[] selectedRows = tbl_summary.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) - .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); + int refSeqColIndex = getResultTable().getColumn("Ref Sequence") + .getModelIndex(); + int[] selectedRows = getResultTable().getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + ArrayList selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { + String pdbIdStr = getResultTable().getValueAt(row, + pdbIdColIndex).toString(); + SequenceI selectedSeq = (SequenceI) getResultTable() + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); if (pdbEntry == null) { pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); - } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + } + pdbEntriesToView[count++] = pdbEntry; + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); 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; + } + 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(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); - pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + ArrayList selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( + row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } + } + 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(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - } + 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()); + } + else + { + pdbEntry.setId(pdbIdStr); + } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } - PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + 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 AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + } + 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(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence }); - } - mainFrame.dispose(); + } + closeAction(preferredHeight); } }).start(); } @@ -849,42 +873,78 @@ public class StructureChooser extends GStructureChooser implements final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar("Launching PDB structure viewer.."); + ssm.setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer")); final StructureViewer sViewer = new StructureViewer(ssm); 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) { - if (seq.getSourceDBRef() == null) - { - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching Database refs.."); - new jalview.ws.DBRefFetcher(sequences, null, null, null, false) - .fetchDBRefs(true); - break; - } - } - } - if (pdbEntriesToView.length > 1) + PDBEntry pdbe = pdbEntriesToView[p++]; + if (pdbe != null && pdbe.getFile() != null) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) + StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); + if (smm != null && smm.length > 0) { - seqsMap.add(new SequenceI[] { seq }); + for (StructureMapping sm : smm) + { + if (sm.getSequence() == seq) + { + continue; + } + } } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structures for selected entries.."); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); } - else + if (seq.getPrimaryDBRefs().size() == 0) { - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structure for " - + pdbEntriesToView[0].getId()); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + seqsWithoutSourceDBRef.add(seq); + continue; + } + } + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y)); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) + { + seqWithoutSrcDBRef[x++] = fSeq; } + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); + dbRefFetcher.fetchDBRefs(true); + } + } + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + 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, alignPanel); + } + else + { + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId())); + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } } /** @@ -918,12 +978,8 @@ public class StructureChooser extends GStructureChooser implements public boolean isStructuresDiscovered() { - return structuresDiscovered; - } - - public void setStructuresDiscovered(boolean structuresDiscovered) - { - this.structuresDiscovered = structuresDiscovered; + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } public Collection getDiscoveredStructuresSet() @@ -943,14 +999,16 @@ public class StructureChooser extends GStructureChooser implements isValidPBDEntry = false; if (txt_search.getText().length() > 0) { + String searchTerm = txt_search.getText().toLowerCase(); + 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(txt_search.getText().toLowerCase() + ")"); + pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); pdbRestCleint = PDBFTSRestClient.getInstance(); wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());