- 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,
- new String(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 = setProtocolState(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 = setProtocolState(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 = setProtocolState(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 = setProtocolState(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 file
- * String
- * @return boolean
- */
- boolean inArchive(String file)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
- if (debug)
- {
- System.err.println("Resource '" + file + "' was "
- + (rtn ? "" : "not") + " located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + file + " "
- + ex);
- return false;
- }
- }
-
- /**
- * If the file is not already in URL format, tries to locate it by resolving
- * as a URL.
- *
- * @param f
- * @return
- */
- String addProtocol(final String f)
- {
- if (f.indexOf("://") != -1)
- {
- // already has URL format
- return f;
- }
-
- /*
- * Try relative to document base
- */
- URL documentBase = getDocumentBase();
- String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- /*
- * Try relative to codebase
- */
- URL codeBase = getCodeBase();
- url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended codebase '" + codeBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- return f;
- }
-
- /**
- * Returns true if an input stream can be opened on the specified URL, else
- * false.
- *
- * @param url
- * @return
- */
- private boolean urlExists(String url)
- {
- InputStream is = null;
- try
- {
- is = new URL(url).openStream();
- if (is != null)
- {
- return true;
- }
- } catch (Exception x)
- {
- // ignore
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- return false;
- }
- }
-
- /**
- * @return the default alignFrame acted on by the public applet methods. May
- * return null with an error message on System.err indicating the
- * fact.
- */
- public AlignFrame getDefaultTargetFrame()
- {
- if (currentAlignFrame != null)
- {
- return currentAlignFrame;
- }
- if (initialAlignFrame != null)
- {
- return initialAlignFrame;
- }
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
- return null;
- }
-
- /**
- * separator used for separatorList
- */
- protected String separator = "" + ((char) 0x00AC); // the default used to be
- // '|' but many sequence
- // IDS include pipes.
-
- /**
- * set to enable the URL based javascript execution mechanism
- */
- public boolean jsfallbackEnabled = false;
-
- /**
- * parse the string into a list
- *
- * @param list
- * @return elements separated by separator
- */
- public String[] separatorListToArray(String list)
- {
- return separatorListToArray(list, separator);
- }
-
- /**
- * parse the string into a list
- *
- * @param list
- * @param separator
- * @return elements separated by separator
- */
- public String[] separatorListToArray(String list, String separator)
- {
- int seplen = separator.length();
- if (list == null || list.equals("") || list.equals(separator))
- {
- return null;
- }
- java.util.Vector jv = new Vector();
- int cp = 0, pos;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (!c.equals(separator))
- {
- jv.addElement(c);
- }
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
- {
- v[i] = (String) jv.elementAt(i);
- }
- jv.removeAllElements();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @return concatenated string
- */
- public String arrayToSeparatorList(String[] list)
- {
- return arrayToSeparatorList(list, separator);
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public String arrayToSeparatorList(String[] list, String separator)
- {
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "" + separator;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
- */
- public String getFeatureGroups()
- {
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
- return lst;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
- * )
- */
- public String getFeatureGroupsOn(AlignFrame alf)
- {
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
- return lst;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
- */
- public String getFeatureGroupsOfState(boolean visible)
- {
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
- * .AlignFrame, boolean)
- */
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
- {
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
- }