X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=aae30b59b8b4ba07944ed2cb2f8911deba207cbe;hb=6f812eb434553c97cccaaaefa35da54afc72bb79;hp=a73405424d5743516bd7ae0325cadfdb209a439e;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a734054..ca2a584 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,297 +1,980 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.bin;
-
-import jalview.gui.*;
-
-import javax.swing.*;
-
-import java.util.Vector;
-
-
-/**
- * Main class for Jalview Application
- *
- *
start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
- *
- * @author $author$
- * @version $Revision$
- */
-public class Jalview
-{
-
- /**
- * main class for Jalview application
- *
- * @param args open filename
- */
- 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"));
-
-
- 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"
- +"-groups FILE\tUse the given file to mark groups on the alignment."
- +"\nThe first lines of the groups file lists the GroupName and GroupColours"
- +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "
- +"\nGROUPNAMEGROUPCOLOUR\n"
- +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUEGROUPNAME\n"
- +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
- +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
- +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\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.");
- System.exit(0);
- }
-
- Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
-
- 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;
- if( !headless )
- {
- try
- {
- UIManager.setLookAndFeel(
- UIManager.getSystemLookAndFeelClassName()
- // UIManager.getCrossPlatformLookAndFeelClassName()
-//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
-//"javax.swing.plaf.metal.MetalLookAndFeel"
-//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
-//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
- );
- }
- catch (Exception ex)
- {
- }
-
- desktop = new Desktop();
- desktop.setVisible(true);
- desktop.discoverer.start();
- }
-
-
- String file = null, protocol = null, format = null, groups=null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
-
- file = aparser.getValue("open");
-
- if (file == null && desktop==null)
- {
- System.out.println("No files to open!");
- System.exit(1);
- }
-
- if(file!=null)
- {
-
- if (!file.startsWith("http://"))
- {
- if (! (new java.io.File(file)).exists())
- {
- System.out.println("Can't find " + file);
- if(headless)
- System.exit(1);
- }
- }
-
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
-
- if (file.endsWith(".jar"))
- format = "Jalview";
- else
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
-
- System.out.println("Opening: " + format + " file " + file);
-
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
-
- groups = aparser.getValue("groups");
- if (groups != null)
- {
- af.parseGroupsFile(groups);
- }
-
- 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());
- }
- }
-
- // We'll only open the default file if the desktop is visible.
- //////////////////////
- if (
- !headless &&
- jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
- {
-
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile.jar");
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
-
- if (file.endsWith(".jar"))
- {
- Jalview2XML.LoadJalviewAlign(file);
- }
- else
- {
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- desktop.LoadFile(file, protocol, format);
- }
- }
- }
-}
-
- 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);
- }
- }
-
- public String getValue(String arg)
- {
- int index = vargs.indexOf(arg);
- String ret = null;
- if (index != -1)
- {
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- }
- return ret;
- }
-
- 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();
- }
-
- }
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+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.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+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.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.URISyntaxException;
+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.LookAndFeel;
+import javax.swing.UIManager;
+
+import com.threerings.getdown.util.LaunchUtil;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
+/**
+ * Main class for Jalview Application
+ *
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ *
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ *
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
+ *
+ * @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 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.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 filename
+ */
+ 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"));
+ // report Jalview version
+ Cache.loadBuildProperties(true);
+
+ 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 -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+ System.exit(0);
+ }
+
+ desktop = null;
+
+ try
+ {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ if (Platform.isAMac())
+ {
+
+ LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel();
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ if (lookAndFeel != null)
+ {
+ try
+ {
+ UIManager.setLookAndFeel(lookAndFeel);
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to set QuaQua look and feel: " + e.toString());
+ }
+ }
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
+ || !UIManager.getLookAndFeel().getClass().toString()
+ .toLowerCase().contains("quaqua"))
+ {
+ try
+ {
+ System.err.println(
+ "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+ UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to reset 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", true))
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
+ }
+
+ if (!headless)
+ {
+ desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
+
+ try
+ {
+ JalviewTaskbar.setTaskbar(this);
+ } catch (Exception e)
+ {
+ System.out.println("Cannot set Taskbar");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Cannot set Taskbar");
+ // t.printStackTrace();
+ }
+
+ 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();
+ }
+
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
+ String file = null, data = null;
+ FileFormatI format = null;
+ DataSourceType protocol = null;
+ FileLoader fileLoader = new FileLoader(!headless);
+
+ 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);
+ }
+ 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);
+
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
+
+ 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.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
+
+ if (cs != null)
+ {
+ 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)
+ {
+ try
+ {
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ NewickFile nf = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, 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)
+ 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)
+ {
+ String outputFormat = aparser.nextValue();
+ 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;
+ }
+
+ 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
+ && 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 = DataSourceType.FILE;
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
+ }
+
+ startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ // extract groovy arguments before anything else.
+ }
+
+ // 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"
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\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 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 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;
+ }
+}