-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.bin;\r
-\r
-import jalview.gui.*;\r
-\r
-import javax.swing.*;\r
-\r
-import java.util.Vector;\r
-\r
-\r
-/**\r
- * Main class for Jalview Application\r
- * <br>\r
- * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Jalview\r
-{\r
-\r
- /**\r
- * main class for Jalview application\r
- *\r
- * @param args open <em>filename</em>\r
- */\r
- public static void main(String[] args)\r
- {\r
- System.out.println("Java version: "+System.getProperty("java.version"));\r
- System.out.println(System.getProperty("os.arch")+" "\r
- +System.getProperty("os.name")+" "\r
- +System.getProperty("os.version"));\r
-\r
-\r
- ArgsParser aparser = new ArgsParser(args);\r
- boolean headless = false;\r
-\r
- if( aparser.contains("help") || aparser.contains("h") )\r
- {\r
- System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"\r
- +"-nodisplay\tRun Jalview without User Interface.\n"\r
- +"-props FILE\tUse the given Jalview properties file instead of users default.\n"\r
- +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"\r
- +"-features FILE\tUse the given file to mark features on the alignment.\n"\r
- +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"\r
- +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"\r
- +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"\r
- +"-msf FILE\tCreate alignment file FILE in MSF format.\n"\r
- +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"\r
- +"-pir FILE\tCreate alignment file FILE in PIR format.\n"\r
- +"-blc FILE\tCreate alignment file FILE in BLC format.\n"\r
- +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"\r
- +"-png FILE\tCreate PNG image FILE from alignment.\n"\r
- +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"\r
- +"-eps FILE\tCreate EPS file FILE from alignment."\r
- +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");\r
- System.exit(0);\r
- }\r
-\r
- Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!\r
-\r
- if (aparser.contains("nodisplay"))\r
- {\r
- System.setProperty("java.awt.headless", "true");\r
- }\r
- if (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true"))\r
- {\r
- headless = true;\r
- }\r
-\r
- try\r
- {\r
- Cache.initLogger();\r
- }\r
- catch (java.lang.NoClassDefFoundError error)\r
- {\r
- error.printStackTrace();\r
- System.out.println(\r
- "\nEssential logging libraries not found."\r
- +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");\r
- System.exit(0);\r
- }\r
-\r
- Desktop desktop = null;\r
- if( !headless )\r
- {\r
- try\r
- {\r
- UIManager.setLookAndFeel(\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
-//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
-//"javax.swing.plaf.metal.MetalLookAndFeel"\r
-//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
-//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
-\r
- );\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- desktop = new Desktop();\r
- desktop.setVisible(true);\r
- desktop.discoverer.start();\r
- }\r
-\r
-\r
- String file = null, protocol = null, format = null, data=null;\r
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();\r
-\r
- file = aparser.getValue("open");\r
-\r
- if (file == null && desktop==null)\r
- {\r
- System.out.println("No files to open!");\r
- System.exit(1);\r
- }\r
-\r
- if(file!=null)\r
- {\r
-\r
- if (!file.startsWith("http://"))\r
- {\r
- if (! (new java.io.File(file)).exists())\r
- {\r
- System.out.println("Can't find " + file);\r
- if(headless)\r
- System.exit(1);\r
- }\r
- }\r
-\r
- protocol = "File";\r
-\r
- if (file.indexOf("http:") > -1)\r
- {\r
- protocol = "URL";\r
- }\r
-\r
- if (file.endsWith(".jar"))\r
- format = "Jalview";\r
- else\r
- format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
-\r
- System.out.println("Opening: " + format + " file " + file);\r
-\r
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
-\r
- // Must maintain ability to use the groups flag\r
- data = aparser.getValue("groups");\r
- if (data != null)\r
- {\r
- af.parseFeaturesFile(data, protocol);\r
- System.out.println("Added "+data);\r
- }\r
- data = aparser.getValue("features");\r
- if (data != null)\r
- {\r
- af.parseFeaturesFile(data, protocol);\r
- System.out.println("Added "+data);\r
- }\r
-\r
- data = aparser.getValue("annotations");\r
- if (data != null)\r
- {\r
- af.loadJalviewDataFile(data);\r
- System.out.println("Added "+data);\r
- }\r
-\r
-\r
- String imageName = "unnamed.png";\r
- while (aparser.getSize() > 1)\r
- {\r
- format = aparser.nextValue();\r
- file = aparser.nextValue();\r
-\r
- if (format.equalsIgnoreCase("png"))\r
- {\r
- af.createPNG(new java.io.File(file));\r
- imageName = (new java.io.File(file)).getName();\r
- System.out.println("Creating PNG image: " + file);\r
- continue;\r
- }\r
- else if (format.equalsIgnoreCase("imgMap"))\r
- {\r
- af.createImageMap(new java.io.File(file), imageName);\r
- System.out.println("Creating image map: " + file);\r
- continue;\r
- }\r
- else if (format.equalsIgnoreCase("eps"))\r
- {\r
- System.out.println("Creating EPS file: " + file);\r
- af.createEPS(new java.io.File(file));\r
- continue;\r
- }\r
-\r
- if (af.saveAlignment(file, format))\r
- System.out.println("Written alignment in " + format +\r
- " format to " + file);\r
- else\r
- System.out.println("Error writing file " + file + " in " + format +\r
- " format!!");\r
-\r
- }\r
-\r
- while (aparser.getSize() > 0)\r
- {\r
- System.out.println("Unknown arg: " + aparser.nextValue());\r
- }\r
- }\r
-\r
- // We'll only open the default file if the desktop is visible.\r
- //////////////////////\r
- if (\r
- !headless\r
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)\r
- )\r
- {\r
-\r
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",\r
- "http://www.jalview.org/examples/exampleFile.jar");\r
-\r
- protocol = "File";\r
-\r
- if (file.indexOf("http:") > -1)\r
- {\r
- protocol = "URL";\r
- }\r
-\r
- if (file.endsWith(".jar"))\r
- {\r
- new Jalview2XML().LoadJalviewAlign(file);\r
- }\r
- else\r
- {\r
- format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
- new jalview.io.FileLoader().LoadFile(file, protocol, format);\r
- }\r
- }\r
- }\r
-}\r
-\r
- class ArgsParser\r
- {\r
- Vector vargs = null;\r
- public ArgsParser(String [] args)\r
- {\r
- vargs = new Vector();\r
- for (int i = 0; i < args.length; i++)\r
- {\r
- String arg = args[i].trim();\r
- if (arg.charAt(0) == '-')\r
- arg = arg.substring(1);\r
- vargs.addElement(arg);\r
- }\r
- }\r
-\r
- public String getValue(String arg)\r
- {\r
- int index = vargs.indexOf(arg);\r
- String ret = null;\r
- if (index != -1)\r
- {\r
- ret = vargs.elementAt(index + 1).toString();\r
- vargs.removeElementAt(index);\r
- vargs.removeElementAt(index);\r
- }\r
- return ret;\r
- }\r
-\r
- public boolean contains(String arg)\r
- {\r
- if(vargs.contains(arg))\r
- {\r
- vargs.removeElement(arg);\r
- return true;\r
- }\r
- else\r
- return false;\r
- }\r
-\r
- public String nextValue()\r
- {\r
- return vargs.remove(0).toString();\r
- }\r
-\r
- public int getSize()\r
- {\r
- return vargs.size();\r
- }\r
-\r
- }\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.bin;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.Constructor;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URL;
+import java.net.URLDecoder;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.gui.*;
+import jalview.util.Platform;
+
+/**
+ * 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
+{
+ static
+ {
+ // grab all the rights we can the JVM
+ Policy.setPolicy(new Policy()
+ {
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ public void refresh()
+ {
+ }
+ });
+ }
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args
+ * open <em>filename</em>
+ */
+ public static void main(String[] args)
+ {
+ System.out.println("Java version: "
+ + System.getProperty("java.version"));
+ System.out.println(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+ if (new Platform().isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ }
+
+ ArgsParser aparser = new ArgsParser(args);
+ boolean headless = false;
+
+ if (aparser.contains("help") || aparser.contains("h"))
+ {
+ 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"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image 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"
+ + "-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)"
+ + "-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");
+ System.exit(0);
+ }
+ Cache.loadProperties(aparser.getValue("props")); // must do this before
+ // anything else!
+ 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 (aparser.contains("nodisplay"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ headless = true;
+ }
+
+ try
+ {
+ Cache.initLogger();
+ } catch (java.lang.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 desktop = null;
+
+ try
+ {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception ex)
+ {
+ }
+
+ if (!headless)
+ {
+ desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
+ desktop.setVisible(true);
+ desktop.startServiceDiscovery();
+ if (!aparser.contains("nousagestats"))
+ {
+ startUsageStats(desktop);
+ }
+ 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);
+ }
+ 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);
+
+ }
+ }
+ }
+ }
+
+ String file = null, protocol = null, format = null, data = null;
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+ Vector 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"), 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 = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
+ if (viprotocol == jalview.io.FormatAdapter.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == jalview.io.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("Processing commandline arguments...", progress=System.currentTimeMillis());
+ }
+ System.out.println("Opening file: " + file);
+
+ if (!file.startsWith("http://"))
+ {
+ if (!(new java.io.File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
+ }
+ }
+
+ protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
+
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ if (af == null)
+ {
+ System.out.println("error");
+ return;
+ }
+
+ data = aparser.getValue("colour", true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
+
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
+
+ if (cs == null)
+ {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+
+ System.out.println("colour is " + data);
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
+ }
+ data = aparser.getValue("features", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
+ }
+
+ data = aparser.getValue("annotations", true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ System.out.println("Added " + data);
+ }
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
+ {
+ af.getViewport().setSortByTree(true);
+ }
+ if (aparser.contains("nosortbytree"))
+ {
+ af.getViewport().setSortByTree(false);
+ }
+ data = aparser.getValue("tree", true);
+ if (data != null)
+ {
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ System.out.println("Added tree " + data);
+ }
+ } 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.
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, new Object[] {desktop,af});
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ groovyscript = null;
+ }
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ 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 jalview.io.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 (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, new Object[] { desktop, 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 startUsageStats(final Desktop desktop)
+ {
+ /**
+ * start a User Config prompt asking if we can log usage statistics.
+ */
+ jalview.gui.PromptUserConfig prompter = new jalview.gui.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()
+ {
+ public void run()
+ {
+ Cache.log
+ .info("Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ }
+ }, new Runnable()
+ {
+ public void run()
+ {
+ Cache.log.info("Not enabling Google Tracking.");
+ }
+ }, null, true);
+ SwingUtilities.invokeLater(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 static void executeGroovyScript(String groovyscript,
+ Object[] jalviewContext)
+ {
+ if (jalviewContext == null)
+ {
+ System.err
+ .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+ }
+ /**
+ * 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 java.io.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;
+ }
+ }
+ }
+ boolean success = false;
+ try
+ {
+ /*
+ * The following code performs the GroovyScriptEngine invocation using
+ * reflection, and is equivalent to this fragment from the embedding
+ * groovy documentation on the groovy site: <code> import
+ * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
+ *
+ * String[] roots = new String[] { "/my/groovy/script/path" };
+ * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
+ * = new Binding(); binding.setVariable("input", "world");
+ * gse.run("hello.groovy", binding); </code>
+ */
+ Class[] bspec;
+ Object[] binding;
+ int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ + ((jalviewContext[1] == null) ? 0 : 1);
+ String cnames[] = new String[]
+ { "Jalview", "currentAlFrame" };
+ bspec = new Class[blen * 2];
+ binding = new Object[blen * 2];
+ blen = 0;
+ ClassLoader cl = null;
+ Map vbinding = new Hashtable();
+ for (int jc = 0; jc < jalviewContext.length; jc++)
+ {
+ if (jalviewContext[jc] != null)
+ {
+ if (cl == null)
+ {
+ cl = jalviewContext[jc].getClass().getClassLoader();
+ }
+ bspec[blen * 2] = String.class;
+ bspec[blen * 2 + 1] = Object.class;
+ binding[blen * 2] = cnames[jc];
+ binding[blen * 2 + 1] = jalviewContext[jc];
+ vbinding.put(cnames[jc], jalviewContext[jc]);
+ blen++;
+ }
+ }
+ Class gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor gbcons;
+ Object gbinding;
+ try
+ {
+ gbcons = gbindingc.getConstructor(Map.class);
+ gbinding = gbcons.newInstance(vbinding);
+ } catch (NoSuchMethodException x)
+ {
+ // old style binding config - using series of string/object values to
+ // setVariable.
+ gbcons = gbindingc.getConstructor(null);
+ gbinding = gbcons.newInstance(null);
+ java.lang.reflect.Method setvar = gbindingc.getMethod(
+ "setVariable", bspec);
+ setvar.invoke(gbinding, binding);
+ }
+ ;
+ Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor gseccons = gsec.getConstructor(new Class[]
+ { URL[].class }); // String[].class });
+ Object gse = gseccons.newInstance(new Object[]
+ { new URL[]
+ { sfile } }); // .toString() } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
+ { String.class, gbindingc });
+ run.invoke(gse, new Object[]
+ { sfile.toString(), gbinding });
+ success = true;
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
+ e.printStackTrace(System.err);
+
+ }
+ if (success && groovyscript.equals("STDIN"))
+ {
+ // delete temp file that we made - but only if it was successfully
+ // executed
+ tfile.delete();
+ }
+ }
+
+ /**
+ * Check commandline for any das server definitions or any fetchfrom switches
+ *
+ * @return vector of DAS source nicknames to retrieve from
+ */
+ private static Vector checkDasArguments(ArgsParser aparser)
+ {
+ Vector 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;
+ boolean seq = false, feat = true;
+ 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();
+ }
+ source.addElement(nickname);
+ }
+ } // 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();
+ }
+ source.addElement(data);
+ }
+ return source;
+ }
+
+ /**
+ * start a feature fetcher for every alignment frame
+ *
+ * @param dasSources
+ */
+ private static FeatureFetcher startFeatureFetching(final Vector 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;
+ }
+}
+
+/**
+ * Notes: this argParser does not distinguish between parameter switches,
+ * parameter values and argument text. If an argument happens to be identical to
+ * a parameter, it will be taken as such (even though it didn't have a '-'
+ * prefixing it).
+ *
+ * @author Andrew Waterhouse and JBP documented.
+ *
+ */
+class ArgsParser
+{
+ Vector vargs = null;
+
+ public ArgsParser(String[] args)
+ {
+ vargs = new Vector();
+ for (int i = 0; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ {
+ arg = arg.substring(1);
+ }
+ vargs.addElement(arg);
+ }
+ }
+
+ /**
+ * check for and remove first occurence of arg+parameter in arglist.
+ *
+ * @param arg
+ * @return return the argument following the given arg if arg was in list.
+ */
+ public String getValue(String arg)
+ {
+ return getValue(arg, false);
+ }
+
+ public String getValue(String arg, boolean utf8decode)
+ {
+ int index = vargs.indexOf(arg);
+ String dc = null, ret = null;
+ if (index != -1)
+ {
+ ret = vargs.elementAt(index + 1).toString();
+ vargs.removeElementAt(index);
+ vargs.removeElementAt(index);
+ if (utf8decode && ret != null)
+ {
+ try
+ {
+ dc = URLDecoder.decode(ret, "UTF-8");
+ ret = dc;
+ } catch (Exception e)
+ {
+ // TODO: log failure to decode
+ }
+ }
+ }
+ return ret;
+ }
+
+ /**
+ * check for and remove first occurence of arg in arglist.
+ *
+ * @param arg
+ * @return true if arg was present in argslist.
+ */
+ public boolean contains(String arg)
+ {
+ if (vargs.contains(arg))
+ {
+ vargs.removeElement(arg);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public String nextValue()
+ {
+ return vargs.remove(0).toString();
+ }
+
+ public int getSize()
+ {
+ return vargs.size();
+ }
+
+}
+
+/**
+ * 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 dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar("DAS features being retrieved...", 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;
+ }
+};
git://source.jalview.org / jalview.git / blobdiff