X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=347c1b2d8ed7b4ec91480bf97acb76b74b7763a3;hb=1b06ffc30dc430351081ecf4bc1515f9448e7ec4;hp=266690eecee2ef9d49e5d5f92e3fc8d2fa0e40f4;hpb=06e3a52df5af8243cdb67c023c8ddd834711ad36;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 266690e..347c1b2 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -75,7 +75,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -180,12 +179,14 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_no_of_structures", + noOfStructuresFound, totalTime)); } else { - mainFrame.setTitle("Structure Chooser - Manual association"); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); @@ -194,7 +195,8 @@ public class StructureChooser extends GStructureChooser errorMsg.append(error).append("\n"); } JOptionPane.showMessageDialog(this, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); } } } @@ -207,7 +209,8 @@ public class StructureChooser extends GStructureChooser if (seq.getDatasetSequence() != null && seq.getDatasetSequence().getAllPDBEntries() != null) { - for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries()) + for (PDBEntry pdbEntry : seq.getDatasetSequence() + .getAllPDBEntries()) { if (pdbEntry.getFile() != null) { @@ -221,7 +224,6 @@ public class StructureChooser extends GStructureChooser tbl_local_pdb.setModel(tableModelx); } - /** * Builds a query string for a given sequences using its DBRef entries * @@ -279,6 +281,11 @@ public class StructureChooser extends GStructureChooser queryBuilder.append("text:").append(seqRef).append(" OR "); } int endIndex = queryBuilder.lastIndexOf(" OR "); + + if (queryBuilder.toString().length() < 6) + { + return null; + } String query = queryBuilder.toString().substring(5, endIndex); return query; } @@ -381,14 +388,13 @@ public class StructureChooser extends GStructureChooser // Update table selection model here tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); } else { - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); @@ -396,8 +402,11 @@ public class StructureChooser extends GStructureChooser { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(null, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + JOptionPane.showMessageDialog( + null, + errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); } } @@ -418,11 +427,11 @@ public class StructureChooser extends GStructureChooser 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) })); + "label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { selectedSequence.getDisplayId(false) })); + "label.load_pdb_file_associate_with_sequence", + selectedSequence.getDisplayId(false))); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) @@ -483,7 +492,8 @@ public class StructureChooser extends GStructureChooser else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { - mainFrame.setTitle(filterTitle); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -535,9 +545,10 @@ public class StructureChooser extends GStructureChooser lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, "No PDB entry found for \'" + txt_search.getText() - + "\'")); + lbl_pdbManualFetchStatus + .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager + .formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) @@ -703,11 +714,9 @@ public class StructureChooser extends GStructureChooser selectedSequence.getDatasetSequence().addPDBId(pdbEntry); } - PDBEntry[] pdbEntriesToView = new PDBEntry[] - { pdbEntry }; + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }); + pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -723,9 +732,8 @@ public class StructureChooser extends GStructureChooser selectedSequence, true, Desktop.instance); launchStructureViewer(ap.getStructureSelectionManager(), - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] - { selectedSequence }); + new PDBEntry[] { fileEntry }, ap, + new SequenceI[] { selectedSequence }); } mainFrame.dispose(); } @@ -744,8 +752,7 @@ public class StructureChooser extends GStructureChooser ArrayList seqsMap = new ArrayList(); for (SequenceI seq : sequences) { - seqsMap.add(new SequenceI[] - { seq }); + seqsMap.add(new SequenceI[] { seq }); } SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); @@ -804,39 +811,45 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + new Thread() { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(txt_search.getText() + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally + public void run() { + errorWarning.setLength(0); + isValidPBDEntry = false; + if (txt_search.getText().length() > 0) + { + List wantedFields = new ArrayList(); + wantedFields.add(PDBDocField.PDB_ID); + PDBRestRequest pdbRequest = new PDBRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(txt_search.getText() + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + pdbRestCleint = new PDBRestClient(); + PDBRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + errorWarning.append(e.getMessage()); + return; + } finally + { + validateSelections(); + } + if (resultList.getSearchSummary() != null + && resultList.getSearchSummary().size() > 0) + { + isValidPBDEntry = true; + } + } validateSelections(); } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) - { - isValidPBDEntry = true; - } - } - validateSelections(); + }.start(); } @Override @@ -860,8 +873,7 @@ public class StructureChooser extends GStructureChooser public class PDBEntryTableModel extends AbstractTableModel { - String[] columns = - { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; private List pdbEntries;