+ boolean haveImport = (vamsasImport != null);
+ if (haveImport)
+ {
+ // if we have a file, start a new session and import it.
+ boolean inSession = false;
+ try
+ {
+ DataSourceType viprotocol = AppletFormatAdapter
+ .checkProtocol(vamsasImport);
+ if (viprotocol == DataSourceType.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == DataSourceType.URL)
+ {
+ inSession = desktop.vamsasImport(new URL(vamsasImport));
+ }
+
+ } catch (Exception e)
+ {
+ System.err.println("Exeption when importing " + vamsasImport
+ + " as a vamsas document.");
+ e.printStackTrace();
+ }
+ if (!inSession)
+ {
+ System.err.println("Failed to import " + vamsasImport
+ + " as a vamsas document.");
+ }
+ else
+ {
+ System.out.println("Imported Successfully into new session "
+ + desktop.getVamsasApplication().getCurrentSession());
+ }
+ }
+ if (vamsasSession != null)
+ {
+ if (vamsasImport != null)
+ {
+ // close the newly imported session and import the Jalview specific
+ // remnants into the new session later on.
+ desktop.vamsasStop_actionPerformed(null);
+ }
+ // now join the new session
+ try
+ {
+ if (desktop.joinVamsasSession(vamsasSession))
+ {
+ System.out.println(
+ "Successfully joined vamsas session " + vamsasSession);
+ }
+ else
+ {
+ System.err.println("WARNING: Failed to join vamsas session "
+ + vamsasSession);
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "ERROR: Failed to join vamsas session " + vamsasSession);
+ e.printStackTrace();
+ }
+ if (vamsasImport != null)
+ {
+ // the Jalview specific remnants can now be imported into the new
+ // session at the user's leisure.
+ Cache.log.info(
+ "Skipping Push for import of data into existing vamsas session."); // TODO:
+ // enable
+ // this
+ // when
+ // debugged
+ // desktop.getVamsasApplication().push_update();
+ }
+ }
+ return haveImport;
+ }
+
+ private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+ FileFormatI format)
+ {
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ // PNG filename
+ // SVG filename
+ // HTML filename
+ // biojsmsa filename
+ String outputFormat = aparser.nextValue();
+ String file = aparser.nextValue();
+ if (outputFormat.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println(
+ "Written alignment in " + format + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in " + format
+ + " format!!");
+ }
+
+ }
+ }
+
+ private static void showUsage()
+ {
+ System.out.println(
+ "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ + "-nodisplay\tRun Jalview without User Interface.\n"
+ + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+ + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+ + "-features FILE\tUse the given file to mark features on the alignment.\n"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
+ + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ + "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-nonews\tTurn off check for Jalview news.\n"
+ + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
+ // +
+ // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
+ // after all other properties files have been read\n\t
+ // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
+ // passed in correctly)"
+ + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ // +
+ // "-vdoc vamsas-document\tImport vamsas document into new
+ // session or join existing session with same URN\n"
+ // + "-vses vamsas-session\tJoin session with given URN\n"
+ + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ }
+
+ private static void startUsageStats(final Desktop desktop)
+ {
+ /**
+ * start a User Config prompt asking if we can log usage statistics.
+ */
+ PromptUserConfig prompter = new PromptUserConfig(
+ Desktop.getDesktopPane(), "USAGESTATS",
+ "Jalview Usage Statistics",
+ "Do you want to help make Jalview better by enabling "
+ + "the collection of usage statistics with Google Analytics ?"
+ + "\n\n(you can enable or disable usage tracking in the preferences)",
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug(
+ "Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ }
+ }, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Not enabling Google Tracking.");
+ }
+ }, null, true);
+ desktop.addDialogThread(prompter);
+ }
+
+ /**
+ * Locate the given string as a file and pass it to the groovy interpreter.
+ *
+ * @param groovyscript
+ * the script to execute
+ * @param jalviewContext
+ * the Jalview Desktop object passed in to the groovy binding as the
+ * 'Jalview' object.
+ */
+ private void executeGroovyScript(String groovyscript, AlignFrame af)
+ {
+ /**
+ * for scripts contained in files
+ */
+ File tfile = null;
+ /**
+ * script's URI
+ */
+ URL sfile = null;
+ if (groovyscript.trim().equals("STDIN"))
+ {
+ // read from stdin into a tempfile and execute it
+ try
+ {
+ tfile = File.createTempFile("jalview", "groovy");
+ PrintWriter outfile = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(tfile)));
+ BufferedReader br = new BufferedReader(
+ new InputStreamReader(System.in));
+ String line = null;
+ while ((line = br.readLine()) != null)
+ {
+ outfile.write(line + "\n");
+ }
+ br.close();
+ outfile.flush();
+ outfile.close();
+
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to read from STDIN into tempfile "
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
+ ex.printStackTrace();
+ return;
+ }
+ try
+ {
+ sfile = tfile.toURI().toURL();
+ } catch (Exception x)
+ {
+ System.err.println(
+ "Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ + tfile.toURI());
+ x.printStackTrace();
+ return;
+ }
+ }
+ else
+ {
+ try
+ {
+ sfile = new URI(groovyscript).toURL();
+ } catch (Exception x)
+ {
+ tfile = new File(groovyscript);
+ if (!tfile.exists())
+ {
+ System.err.println("File '" + groovyscript + "' does not exist.");
+ return;
+ }
+ if (!tfile.canRead())
+ {
+ System.err.println("File '" + groovyscript + "' cannot be read.");
+ return;
+ }
+ if (tfile.length() < 1)
+ {
+ System.err.println("File '" + groovyscript + "' is empty.");
+ return;
+ }
+ try
+ {
+ sfile = tfile.getAbsoluteFile().toURI().toURL();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to create a file URL for "
+ + tfile.getAbsoluteFile());
+ return;
+ }
+ }
+ }
+ try
+ {
+ Map<String, Object> vbinding = new HashMap<>();
+ vbinding.put("Jalview", this);
+ if (af != null)
+ {
+ vbinding.put("currentAlFrame", af);
+ }
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
+ {
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
+ e.printStackTrace(System.err);
+
+ }
+ }
+
+ public AlignFrame[] getAlignFrames()
+ {
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
+
+ }
+
+ /**
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
+ */
+ public void quit()
+ {
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
+ }
+
+ if (desktop != null)
+ {
+ desktop.quit();
+ }
+ else
+ {
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+ String id = Cache.getProperty("Info.j2sAppletID");
+ if (id == null)
+ {
+ id = "jalview";
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
+
+ /**
+ * Handle all JalviewLite applet parameters
+ *
+ * @param aparser
+ * @param af
+ */
+ private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+ {
+ JalviewApp app = new JalviewApp()
+ {
+
+ private boolean alignPDBStructures; // From JalviewLite; not implemented
+
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+ private Hashtable<String, int[]> jshashes;
+
+ @Override
+ public String getParameter(String name)
+ {
+ return aparser.getAppletValue(name, null);
+ }
+
+ @Override
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ return ((stn = getParameter(name)) == null ? def
+ : "true".equalsIgnoreCase(stn));
+ }
+
+ /**
+ * Get the applet-like document base even though this is an application.
+ */
+ @Override
+ public URL getDocumentBase()
+ {
+ return Platform.getDocumentBase();
+ }
+
+ /**
+ * Get the applet-like code base even though this is an application.
+ */
+ @Override
+ public URL getCodeBase()
+ {
+ return Platform.getCodeBase();
+ }
+
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return af.getViewport();
+ }
+
+ /**
+ * features
+ *
+ */
+ @Override
+ public boolean parseFeaturesFile(String filename,
+ DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
+ }
+
+ /**
+ * scorefile
+ *
+ */
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ af.loadJalviewDataFile(sScoreFile, null, null, null);
+ return true;
+ }
+
+ /**
+ * annotations, jpredfile, jnetfile
+ *
+ */
+ @Override
+ public void updateForAnnotations()
+ {
+ af.updateForAnnotations();
+ }
+
+ @Override
+ public void loadTree(NewickFile fin, String treeFile)
+ throws IOException
+ {
+ // n/a -- already done by standard Jalview command line processing
+ }
+
+ @Override
+ public void setAlignPdbStructures(boolean defaultParameter)
+ {
+ alignPDBStructures = true;
+ }
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
+ }
+
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ af.setFeatureGroupState(groups, state);
+ }
+
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ System.err.println(
+ "Jalview applet interface alignedStructureView not implemented");
+ }
+
+ @Override
+ public void newFeatureSettings()
+ {
+ System.err.println(
+ "Jalview applet interface newFeatureSettings not implemented");
+ }
+
+ private Vector<Runnable> jsExecQueue;
+
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+ {
+ jsFunctionExec = exec;
+ return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+ : jsExecQueue);
+ }
+
+ @Override
+ public AppletContext getAppletContext()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener mouseOverStructureListener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source, Object alignFrame)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String arrayToSeparatorList(String[] array)
+ {
+ return appLoader.arrayToSeparatorList(array);
+ }
+
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
+ {
+ return (jshashes == null
+ ? (jshashes = new Hashtable<>())
+ : jshashes);
+ }
+
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+ {
+ return (jsmessages == null
+ ? (jsmessages = new Hashtable<>())
+ : jsmessages);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ AlignFrame af;
+ if (source instanceof jalview.gui.AlignViewport
+ && source == (af = getCurrentAlignFrame()).getViewport())
+ {
+ // should be valid if it just generated an event!
+ return af;
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+ }
+
+ };
+
+ appLoader = new JalviewAppLoader(true);
+ appLoader.load(app);
+ }
+
+ @Override
+ public String getSelectedSequences()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequences(String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void highlightIn(AlignFrameI alf,
+ String sequenceId, String position, String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds,
+ String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds,
+ String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(
+ AlignFrameI alf, String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrder()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderAlignmentBy(AlignFrameI alf,
+ String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf,
+ String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrameI alf,
+ String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean loadFeaturesFrom(AlignFrameI alf,
+ String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String getFeatures(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeaturesFrom(AlignFrameI alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotation()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newView()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newView(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI loadAlignment(String text,
+ String title)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setMouseoverListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setMouseoverListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setStructureListener(String listener, String modelSet)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void removeJavascriptListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean addPdbFile(AlignFrameI alFrame,
+ String sequenceId, String pdbEntryString, String pdbFile)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void scrollViewToIn(AlignFrameI alf,
+ String topRow, String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToRowIn(AlignFrameI alf,
+ String topRow)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToColumnIn(AlignFrameI alf,
+ String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf,
+ boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setFeatureGroupStateOn(AlignFrameI alf,
+ String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setSeparator(String separator)
+ {
+ // TODO Auto-generated method stub
+