-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-package jalview.bin;\r
-\r
-import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import jalview.io.*;\r
-\r
-\r
-public class Jalview extends JApplet\r
-{\r
- public static JApplet applet;\r
- Desktop frame;\r
- public void init()\r
- {\r
- applet = this;\r
-\r
- frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- applet.stop();\r
- applet.destroy();\r
- }\r
- });\r
-\r
- String file = getParameter("alignment");\r
-\r
- if(file!=null)\r
- {\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
- }\r
-\r
- public void destroy()\r
- {\r
- if(applet!=null)\r
- applet.stop();\r
- else\r
- System.exit(0);\r
- frame.setVisible(false);\r
- }\r
-\r
- public static void main(String[] args) {\r
-\r
- Cache.loadProperties();\r
-\r
- try{\r
- UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
- // "javax.swing.plaf.multi.MultiLookAndFeel"\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
- );\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- // JFrame.setDefaultLookAndFeelDecorated(true);\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
-\r
-\r
- if(args!=null && args.length>0)\r
- {\r
- String file = args[0];\r
- String protocol = "File";\r
- if(file.indexOf("http:")>-1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
-\r
- }\r
-\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URL;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
+
+import javax.swing.UIManager;
+
+/**
+ * Main class for Jalview Application <br>
+ * <br>
+ * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
+{
+ /*
+ * singleton instance of this class
+ */
+ private static Jalview instance;
+
+ private Desktop desktop;
+
+ public static AlignFrame currentAlignFrame;
+
+ static
+ {
+ // grab all the rights we can the JVM
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
+
+ /**
+ * keep track of feature fetching tasks.
+ *
+ * @author JimP
+ *
+ */
+ class FeatureFetcher
+ {
+ /*
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
+ */
+
+ private int queued = 0;
+
+ private int running = 0;
+
+ public FeatureFetcher()
+ {
+
+ }
+
+ public void addFetcher(final AlignFrame af,
+ final Vector<String> dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
+ af.featureSettings_actionPerformed(null);
+ af.featureSettings.fetchDasFeatures(dasSources, true);
+ af.setProgressBar(null, id);
+ synchronized (us)
+ {
+ running--;
+ }
+ }
+ }).start();
+ }
+
+ public synchronized boolean allFinished()
+ {
+ return queued == 0 && running == 0;
+ }
+
+ }
+
+ public static Jalview getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args
+ * open <em>filename</em>
+ */
+ public static void main(String[] args)
+ {
+ instance = new Jalview();
+ instance.doMain(args);
+ }
+
+ /**
+ * @param args
+ */
+ void doMain(String[] args)
+ {
+ System.setSecurityManager(null);
+ System.out.println("Java version: "
+ + System.getProperty("java.version"));
+ System.out.println(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ ArgsParser aparser = new ArgsParser(args);
+ boolean headless = false;
+
+ if (aparser.contains("help") || aparser.contains("h"))
+ {
+ showUsage();
+ System.exit(0);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
+ // anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid jabaws parameter: " + jabawsUrl
+ + " ignored");
+ }
+ }
+
+ String defs = aparser.getValue("setprop");
+ while (defs != null)
+ {
+ int p = defs.indexOf('=');
+ if (p == -1)
+ {
+ System.err.println("Ignoring invalid setprop argument : " + defs);
+ }
+ else
+ {
+ System.out.println("Executing setprop argument: " + defs);
+ // DISABLED FOR SECURITY REASONS
+ // TODO: add a property to allow properties to be overriden by cli args
+ // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ }
+ defs = aparser.getValue("setprop");
+ }
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ headless = true;
+ }
+ System.setProperty("http.agent",
+ "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+ try
+ {
+ Cache.initLogger();
+ } catch (NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out
+ .println("\nEssential logging libraries not found."
+ + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.exit(0);
+ }
+
+ desktop = null;
+
+ try
+ {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception ex)
+ {
+ }
+ if (Platform.isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ try
+ {
+ UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel());
+ } catch (Throwable e)
+ {
+ System.err.println("Failed to set QuaQua look and feel: "
+ + e.toString());
+ }
+ }
+
+ /*
+ * configure 'full' SO model if preferences say to,
+ * else use the default (SO Lite)
+ */
+ if (Cache.getDefault("USE_FULL_SO", false))
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
+ }
+
+ if (!headless)
+ {
+ desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
+ desktop.setVisible(true);
+ desktop.startServiceDiscovery();
+ if (!aparser.contains("nousagestats"))
+ {
+ startUsageStats(desktop);
+ }
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
+ if (!aparser.contains("noquestionnaire"))
+ {
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ Cache.log.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug("Starting questionnaire with default url: "
+ + defurl);
+ desktop.checkForQuestionnaire(defurl);
+ }
+ }
+ }
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
+ }
+
+ BioJsHTMLOutput.updateBioJS();
+ }
+
+ String file = null, protocol = null, format = null, data = null;
+ FileLoader fileLoader = new FileLoader(!headless);
+ Vector<String> getFeatures = null; // vector of das source nicknames to
+ // fetch
+ // features from
+ // loading is done.
+ String groovyscript = null; // script to execute after all loading is
+ // completed one way or another
+ // extract groovy argument and execute if necessary
+ groovyscript = aparser.getValue("groovy", true);
+ file = aparser.getValue("open", true);
+
+ if (file == null && desktop == null)
+ {
+ System.out.println("No files to open!");
+ System.exit(1);
+ }
+ String vamsasImport = aparser.getValue("vdoc");
+ String vamsasSession = aparser.getValue("vsess");
+ if (vamsasImport != null || vamsasSession != null)
+ {
+ if (desktop == null || headless)
+ {
+ System.out
+ .println("Headless vamsas sessions not yet supported. Sorry.");
+ System.exit(1);
+ }
+ // if we have a file, start a new session and import it.
+ boolean inSession = false;
+ if (vamsasImport != null)
+ {
+ try
+ {
+ String viprotocol = AppletFormatAdapter
+ .checkProtocol(vamsasImport);
+ if (viprotocol == jalview.io.FormatAdapter.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == FormatAdapter.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();
+ }
+ }
+ }
+ long progress = -1;
+ // Finally, deal with the remaining input data.
+ if (file != null)
+ {
+ if (!headless)
+ {
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
+ progress = System.currentTimeMillis());
+ }
+ System.out.println("CMD [-open " + file + "] executed successfully!");
+
+ if (!file.startsWith("http://"))
+ {
+ if (!(new File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
+ }
+ }
+
+ protocol = AppletFormatAdapter.checkProtocol(file);
+
+ format = new IdentifyFile().identify(file, protocol);
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ if (af == null)
+ {
+ System.out.println("error");
+ }
+ else
+ {
+ setCurrentAlignFrame(af);
+ data = aparser.getValue("colour", true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
+
+ ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ .getViewport().getAlignment(), data);
+
+ if (cs == null)
+ {
+ UserColourScheme ucs = new UserColourScheme("white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
+ }
+ data = aparser.getValue("features", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
+ }
+
+ data = aparser.getValue("annotations", true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
+ }
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
+ {
+ af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("CMD [-sortbytree] executed successfully!");
+ }
+ }
+ if (aparser.contains("no-annotation"))
+ {
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
+ }
+ if (aparser.contains("nosortbytree"))
+ {
+ af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
+ }
+ data = aparser.getValue("tree", true);
+ if (data != null)
+ {
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
+ fin = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ }
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
+
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures != null)
+ {
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff != null)
+ {
+ while (!ff.allFinished() || af.operationInProgress())
+ {
+ // wait around until fetching is finished.
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+
+ }
+ }
+ }
+ getFeatures = null; // have retrieved features - forget them now.
+ }
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
+ }
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ new HtmlSvgOutput(new File(file), af.alignPanel);
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("biojsmsa"))
+ {
+ BioJsHTMLOutput.updateBioJS();
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: "
+ + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ if (af.saveAlignment(file, format))
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
+ }
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
+ }
+ }
+ AlignFrame startUpAlframe = null;
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ // ////////////////////
+
+ if (!headless && file == null && vamsasImport == null
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ {
+ file = jalview.bin.Cache.getDefault(
+ "STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ }
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
+
+ startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ getFeatures = checkDasArguments(aparser);
+ // extract groovy arguments before anything else.
+ }
+ // If the user has specified features to be retrieved,
+ // or a groovy script to be executed, do them if they
+ // haven't been done already
+ // fetch features for the default alignment
+ if (getFeatures != null)
+ {
+ if (startUpAlframe != null)
+ {
+ startFeatureFetching(getFeatures);
+ }
+ }
+ // Once all other stuff is done, execute any groovy scripts (in order)
+ if (groovyscript != null)
+ {
+ if (Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, startUpAlframe);
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ }
+ // and finally, turn off batch mode indicator - if the desktop still exists
+ if (desktop != null)
+ {
+ if (progress != -1)
+ {
+ desktop.setProgressBar(null, progress);
+ }
+ desktop.setInBatchMode(false);
+ }
+ }
+
+ 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"
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\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.desktop,
+ "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<String, Object>();
+ 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);
+
+ }
+ }
+
+ /**
+ * Check commandline for any das server definitions or any fetchfrom switches
+ *
+ * @return vector of DAS source nicknames to retrieve from
+ */
+ private static Vector<String> checkDasArguments(ArgsParser aparser)
+ {
+ Vector<String> source = null;
+ String data;
+ String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
+ while ((data = aparser.getValue("dasserver", true)) != null)
+ {
+ String nickname = null;
+ String url = null;
+ int pos = data.indexOf('=');
+ // determine capabilities
+ if (pos > 0)
+ {
+ nickname = data.substring(0, pos);
+ }
+ url = data.substring(pos + 1);
+ if (url != null
+ && (url.startsWith("http:") || url
+ .startsWith("sequence:http:")))
+ {
+ if (nickname == null)
+ {
+ nickname = url;
+ }
+ if (locsources == null)
+ {
+ locsources = "";
+ }
+ else
+ {
+ locsources += "\t";
+ }
+ locsources = locsources + nickname + "|" + url;
+ System.err
+ .println("NOTE! dasserver parameter not yet really supported (got args of "
+ + nickname + "|" + url);
+ if (source == null)
+ {
+ source = new Vector<String>();
+ }
+ source.addElement(nickname);
+ }
+ System.out.println("CMD [-dasserver " + data
+ + "] executed successfully!");
+ } // loop until no more server entries are found.
+ if (locsources != null && locsources.indexOf('|') > -1)
+ {
+ Cache.log.debug("Setting local source list in properties file to:\n"
+ + locsources);
+ Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
+ }
+ while ((data = aparser.getValue("fetchfrom", true)) != null)
+ {
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
+ {
+ source = new Vector<String>();
+ }
+ source.addElement(data);
+ }
+ return source;
+ }
+
+ /**
+ * start a feature fetcher for every alignment frame
+ *
+ * @param dasSources
+ */
+ private FeatureFetcher startFeatureFetching(
+ final Vector<String> dasSources)
+ {
+ FeatureFetcher ff = new FeatureFetcher();
+ AlignFrame afs[] = Desktop.getAlignFrames();
+ if (afs == null || afs.length == 0)
+ {
+ return null;
+ }
+ for (int i = 0; i < afs.length; i++)
+ {
+ ff.addFetcher(afs[i], dasSources);
+ }
+ return ff;
+ }
+
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ 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 (desktop != null)
+ {
+ desktop.quit();
+ }
+ else
+ {
+ System.exit(0);
+ }
+ }
+
+ public static AlignFrame getCurrentAlignFrame()
+ {
+ return Jalview.currentAlignFrame;
+ }
+
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ {
+ Jalview.currentAlignFrame = currentAlignFrame;
+ }
+}