+ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
+ if (tp == null)
+ {
+ tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
+ if (tree.getId() != null)
+ {
+ // perhaps bind the tree id to something ?
+ }
+ }
+ else
+ {
+ // update local tree attributes ?
+ // TODO: should check if tp has been manipulated by user - if so its
+ // settings shouldn't be modified
+ tp.setTitle(tree.getTitle());
+ tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
+ .getWidth(), tree.getHeight()));
+ tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ // views'
+ // works still
+ tp.treeCanvas.av = av; // af.viewport;
+ tp.treeCanvas.ap = ap; // af.alignPanel;
+
+ }
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
+
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
+
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+ .getFontStyle(), tree.getFontSize()));
+ }
+ else
+ {
+ tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), tree.getFontSize()));
+ }
+
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
+
+ tp.treeCanvas.threshold = tree.getThreshold();
+
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // //LOAD STRUCTURES
+ if (loadTreesAndStructures)
+ {
+ // run through all PDB ids on the alignment, and collect mappings between
+ // jmol view ids and all sequences referring to it
+ Hashtable<String, Object[]> jmolViewIds = new Hashtable();
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+ {
+ // check to see if we haven't already created this structure view
+ String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
+ : ids[p].getStructureState(s).getViewId()
+ + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : ids[p].getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setId(ids[p].getId());
+
+ int x = ids[p].getStructureState(s).getXpos();
+ int y = ids[p].getStructureState(s).getYpos();
+ int width = ids[p].getStructureState(s).getWidth();
+ int height = ids[p].getStructureState(s).getHeight();
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
+ .get(JSEQ[i].getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!jmolViewIds.containsKey(sviewid))
+ {
+ jmolViewIds.put(sviewid, new Object[]
+ { new int[]
+ { x, y, width, height }, "",
+ new Hashtable<String, Object[]>(), new boolean[]
+ { false, false, true } });
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
+ }
+
+ // assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
+ Object[] jmoldat = jmolViewIds.get(sviewid);
+ ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
+ .hasAlignwithAlignPanel() ? ids[p].getStructureState(
+ s).getAlignwithAlignPanel() : false;
+ // never colour by linked panel if not specified
+ ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
+ .hasColourwithAlignPanel() ? ids[p]
+ .getStructureState(s).getColourwithAlignPanel()
+ : false;
+ // default for pre-2.7 projects is that Jmol colouring is enabled
+ ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s)
+ .hasColourByJmol() ? ids[p].getStructureState(s)
+ .getColourByJmol() : true;
+
+ if (((String) jmoldat[1]).length() < ids[p]
+ .getStructureState(s).getContent().length())
+ {
+ {
+ jmoldat[1] = ids[p].getStructureState(s).getContent();
+ }
+ }
+ if (ids[p].getFile() != null)
+ {
+ File mapkey=new File(ids[p].getFile());
+ Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+ .get(mapkey);
+ if (seqstrmaps == null)
+ {
+ ((Hashtable) jmoldat[2]).put(
+ mapkey,
+ seqstrmaps = new Object[]
+ { pdbFile, ids[p].getId(), new Vector(),
+ new Vector() });
+ }
+ if (!((Vector) seqstrmaps[2]).contains(seq))
+ {
+ ((Vector) seqstrmaps[2]).addElement(seq);
+ // ((Vector)seqstrmaps[3]).addElement(n) :
+ // in principle, chains
+ // should be stored here : do we need to
+ // TODO: store and recover seq/pdb_id :
+ // chain mappings
+ }
+ }
+ else
+ {
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ warn(errorMessage);
+ }
+ }
+ }
+ }
+ }
+ {
+
+ // Instantiate the associated Jmol views
+ for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
+ {
+ String sviewid = entry.getKey();
+ Object[] svattrib = entry.getValue();
+ int[] geom = (int[]) svattrib[0];
+ String state = (String) svattrib[1];
+ Hashtable<File, Object[]> oldFiles = (Hashtable<File, Object[]>) svattrib[2];
+ final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
+ int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
+ // collate the pdbfile -> sequence mappings from this view
+ Vector<String> pdbfilenames = new Vector<String>();
+ Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
+ Vector<String> pdbids = new Vector<String>();
+
+ // Search to see if we've already created this Jmol view
+ AppJmol comp = null;
+ JInternalFrame[] frames = null;
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ frames = null;
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception f)
+ {
+ }
+ ;
+ }
+ } while (frames == null);
+ // search for any Jmol windows already open from other
+ // alignment views that exactly match the stored structure state
+ for (int f = 0; comp == null && f < frames.length; f++)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ if (sviewid != null
+ && ((AppJmol) frames[f]).getViewId().equals(sviewid))
+ {
+ // post jalview 2.4 schema includes structure view id
+ comp = (AppJmol) frames[f];
+ }
+ else if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = (AppJmol) frames[f];
+ }
+ }
+ }
+
+ if (comp == null)
+ {
+ // create a new Jmol window.
+ // First parse the Jmol state to translate filenames loaded into the
+ // view, and record the order in which files are shown in the Jmol
+ // view, so we can add the sequence mappings in same order.
+ StringBuffer newFileLoc = null;
+ int cp = 0, ncp, ecp;
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ if (newFileLoc == null)
+ {
+ newFileLoc = new StringBuffer();
+ }
+ do {
+ // look for next filename in load statement
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform.escapeString((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp=state.indexOf("/*file*/",cp))>-1);
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err
+ .print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuffer(state);
+ newFileLoc.append("; load append ");
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ Object[] filedat = oldFiles.get(id);
+ String nfilename;
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append((String) filedat[0]);
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ if (newFileLoc != null)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
+ histbug);
+ String val = (diff == -1) ? null : newFileLoc.substring(
+ histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
+ {
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ final String[] pdbf = pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = pdbids
+ .toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString(), vid = sviewid;
+ final AlignFrame alf = af;
+ final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
+ width, height);
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ AppJmol sview = null;
+ try
+ {
+ sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ useinJmolsuperpos, usetoColourbyseq,
+ jmolColouring, fileloc, rect, vid);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id "
+ + id, (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+
+ }
+ else
+ // if (comp != null)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
+
+ // add mapping for sequences in this view to an already open Jmol
+ // instance
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ Object[] filedat = oldFiles.get(id);
+ String pdbFile = (String) filedat[0];
+ SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]);
+ comp.jmb.ssm.setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ comp.jmb.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the Jmol view
+ comp.addAlignmentPanel(ap);
+ if (useinJmolsuperpos)
+ {
+ comp.useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ comp.excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ comp.useAlignmentPanelForColourbyseq(ap,
+ !jmolColouring);
+ }
+ else
+ {
+ comp.excludeAlignmentPanelForColourbyseq(ap);
+ }
+ }
+ }
+ }
+ }
+ // and finally return.
+ return af;
+ }
+
+ AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
+ Alignment al, JalviewModelSequence jms, Viewport view,
+ String uniqueSeqSetId, String viewId,
+ ArrayList<JvAnnotRow> autoAlan)
+ {
+ AlignFrame af = null;
+ af = new AlignFrame(al, view.getWidth(), view.getHeight(),
+ uniqueSeqSetId, viewId);
+
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
+ }
+
+ af.viewport.gatherViewsHere = view.getGatheredViews();
+
+ if (view.getSequenceSetId() != null)
+ {
+ jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
+ .get(uniqueSeqSetId);
+
+ af.viewport.setSequenceSetId(uniqueSeqSetId);
+ if (av != null)
+ {
+ // propagate shared settings to this new view
+ af.viewport.historyList = av.historyList;
+ af.viewport.redoList = av.redoList;
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ }
+ // TODO: check if this method can be called repeatedly without
+ // side-effects if alignpanel already registered.
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ // apply Hidden regions to view.
+ if (hiddenSeqs != null)
+ {
+ for (int s = 0; s < JSEQ.length; s++)
+ {
+ jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
+
+ for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ {
+ hidden.addSequence(
+ al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ }
+ af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
+ }
+
+ jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
+ .size()];
+
+ for (int s = 0; s < hiddenSeqs.size(); s++)
+ {
+ hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+ }
+
+ af.viewport.hideSequence(hseqs);
+
+ }
+ // recover view properties and display parameters
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
+
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
+
+ af.viewport.setColourText(view.getShowColourText());