- /**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadPdbFiles(AlignFrame alignFrame)
- {
- boolean result = false;
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
- * related to JAL-434
- */
-
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
-
- int pdbFileCount = 0;
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector pdbs = new Vector();
- // create a lazy matcher if we're asked to
- jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
- alignFrame.getAlignViewport().getAlignment()
- .getSequencesArray()) : null;
-
- String param;
- do
- {
- if (pdbFileCount > 0)
- {
- param = applet.getParameter("PDBFILE" + pdbFileCount);
- }
- else
- {
- param = applet.getParameter("PDBFILE");
- }
-
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- {
- seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment().findName(sequence)
- : matcher.findIdMatch(sequence) };
- }
-
- }
- else
- {
- param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
-
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.add(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.add(matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment()
- .findName(seqstring) : matcher.findIdMatch(seqstring));
- }
-
- seqs = tmp.toArray(new SequenceI[tmp.size()]);
- if (tmp2.size() == tmp.size())
- {
- chains = tmp2.toArray(new String[tmp2.size()]);
- }
- }
- param = resolveFileProtocol(param);
- // TODO check JAL-357 for files in a jar (CLASSLOADER)
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- if (!alignPdbStructures)
- {
- alignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
- }
- else
- {
- pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
- }
- }
- }
-
- pdbFileCount++;
- } while (param != null || pdbFileCount < 10);
- if (pdbs.size() > 0)
- {
- SequenceI[][] seqs = new SequenceI[pdbs.size()][];
- PDBEntry[] pdb = new PDBEntry[pdbs.size()];
- String[][] chains = new String[pdbs.size()][];
- String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
- {
- Object[] o = (Object[]) pdbs.elementAt(pdbsi);
- pdb[pdbsi] = (PDBEntry) o[0];
- seqs[pdbsi] = (SequenceI[]) o[1];
- chains[pdbsi] = (String[]) o[2];
- protocols[pdbsi] = (String) o[3];
- }
- alignFrame.alignedStructureView(applet, pdb, seqs, chains,
- protocols);
- result = true;
- }
- return result;
- }
-
- /**
- * Load in a Jnetfile if specified by parameter. Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadJnetFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("jnetfile");
- if (param != null)
- {
- try
- {
- param = resolveFileProtocol(param);
- JPredFile predictions = new JPredFile(param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- alignFrame.viewport.getAlignment(), 0, false);
- // false == do not add sequence profile from concise output
- SequenceI repseq = alignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- alignFrame.viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
- cs.hideInsertionsFor(repseq);
- alignFrame.viewport.setColumnSelection(cs);
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Load annotations if specified by parameter. Returns true if loaded, else
- * false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadAnnotations(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("annotations");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- param, protocol))
- {
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- }
- else
- {
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
- }
- }
- return result;
- }
-
- /**
- * Load features file and view settings as specified by parameters. Returns
- * true if features were loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadFeatures(AlignFrame alignFrame)
- {
- boolean result = false;
- // ///////////////////////////
- // modify display of features
- // we do this before any features have been loaded, ensuring any hidden
- // groups are hidden when features first displayed
- //
- // hide specific groups
- //
- String param = applet.getParameter("hidefeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), false);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = applet.getParameter("showfeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), true);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
- }
- // and now load features
- param = applet.getParameter("features");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- result = alignFrame.parseFeaturesFile(param, protocol);
- }
-
- param = applet.getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase(TRUE))
- {
- alignFrame.viewport.setShowSequenceFeatures(true);
- new FeatureSettings(alignFrame.alignPanel);
- }
- return result;
- }
-
- /**
- * Load a score file if specified by parameter. Returns true if file was
- * loaded, else false.
- *
- * @param alignFrame
- */
- protected boolean loadScoreFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String sScoreFile = applet.getParameter("scoreFile");
- if (sScoreFile != null && !"".equals(sScoreFile))
- {
- try
- {
- if (debug)
- {
- System.err
- .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
- }
- result = alignFrame.loadScoreFile(sScoreFile);
- if (!result)
- {
- System.err
- .println("Failed to parse T-COFFEE parameter as a valid score file ('"
- + sScoreFile + "')");
- }
- } catch (Exception e)
- {
- System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
- sScoreFile, e.getMessage());
- }
- }
- return result;
- }
-
- /**
- * Load a tree for the alignment if specified by parameter. Returns true if
- * a tree was loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadTree(AlignFrame alignFrame)
- {
- boolean result = false;
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
- {
- treeFile = applet.getParameter("treeFile");
- }
-
- if (treeFile != null)
- {
- try
- {
- treeFile = resolveFileProtocol(treeFile);
- NewickFile fin = new NewickFile(treeFile, protocol);
- fin.parse();
-
- if (fin.getTree() != null)
- {
- alignFrame.loadTree(fin, treeFile);
- result = true;
- dbgMsg("Successfully imported tree.");
- }
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Discovers whether the given file is in the Applet Archive
- *
- * @param f
- * String
- * @return boolean
- */
- boolean inArchive(String f)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
- if (debug)
- {
- System.err.println("Resource '" + f + "' was "
- + (rtn ? "" : "not ") + "located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + f + " " + ex);
- return false;
- }
- }