+ public class PDBEntryTableModel extends AbstractTableModel
+ {
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
+
+ private List<CachedPDB> pdbEntries;
+
+ public PDBEntryTableModel(List<CachedPDB> 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)
+ {
+ if (!Platform.isHeadless() && progressBar != null)
+ progressBar.setProgressBar(message, id);
+ }
+
+ @Override
+ public void registerHandler(long id, IProgressIndicatorHandler handler)
+ {
+ if (progressBar != null)
+ progressBar.registerHandler(id, handler);
+ }
+
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar == null ? false : 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;
+ }
+
+ /**
+ * Open a single structure file for a given sequence
+ */
+ public static void openStructureFileForSequence(
+ StructureSelectionManager ssm, StructureChooser sc,
+ AlignmentPanel ap, SequenceI seq, boolean prompt,
+ String sFilename, TFType tft, String paeFilename,
+ boolean doXferSettings)
+ {
+ openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
+ paeFilename, false, true, doXferSettings, null);
+ }
+
+ public static StructureViewer openStructureFileForSequence(
+ StructureSelectionManager ssm, StructureChooser sc,
+ AlignmentPanel ap, SequenceI seq, boolean prompt,
+ String sFilename, TFType tft, String paeFilename,
+ boolean forceHeadless, boolean showRefAnnotations,
+ boolean doXferSettings, ViewerType viewerType)
+ {
+ StructureViewer sv = null;
+ boolean headless = forceHeadless;
+ if (sc == null)
+ {
+ // headless = true;
+ prompt = false;
+ // suppress structure viewer's external service queries
+ sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,true);
+ }
+ if (ssm == null)
+ {
+ ssm = ap.getStructureSelectionManager();
+ }
+
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+ tft, paeFilename, doXferSettings);
+
+ // if headless, "false" in the sc constructor above will avoid GUI behaviour
+ // in sc.launchStructureViewer()
+ if (!headless && !(viewerType == null))
+ {
+ sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[]
+ { seq }, viewerType);
+ }
+
+ sc.mainFrame.dispose();
+
+ if (showRefAnnotations)
+ {
+ showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
+
+ return sv;
+ }
+
+ public static void showReferenceAnnotationsForSequence(AlignFrame af,
+ SequenceI sequence)
+ {
+ AlignViewport av = af.getCurrentView();
+ AlignmentI al = av.getAlignment();
+
+ List<SequenceI> forSequences = new ArrayList<>();
+ forSequences.add(sequence);
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, null,
+ candidates, al);
+ final SequenceGroup selectionGroup = av.getSelectionGroup();
+ AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup);
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ // required to readjust the height and position of the PAE
+ // annotation
+ ap.adjustAnnotationHeight();
+ }
+
+ }