X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=c1354c70514c1041a082d42fd4f21c7008110a90;hb=a84906104415e9e65713af39a225090ebd7beff0;hp=5dc6c817da43d237aa12e405008727a10e3c4e3f;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5dc6c81..c1354c7 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,1044 +1,834 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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.lang.reflect.Constructor;
+import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URISyntaxException;
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 java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
-import javax.swing.*;
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
-import jalview.gui.*;
-import jalview.util.Platform;
+import com.threerings.getdown.util.LaunchUtil;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
/**
* Main class for Jalview Application
*
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * 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
{
- 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 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"));
- 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);
- }
- if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
- {
- System.setProperty("java.awt.headless", "true");
- headless=true;
- }
- 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 (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 (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);
-
- }
- }
- }
- desktop.checkForNews();
- }
-
- 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");
- }
- else
- {
-
- 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);
- 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 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: 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);
- */
- 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();
- }
-
+ /*
+ * 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", false)) {
+ 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);
+ }
+ 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 {
+ DataSourceType viprotocol = AppletFormatAdapter.checkProtocol(vamsasImport);
+ if (viprotocol == DataSourceType.FILE) {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ } else if (viprotocol == DataSourceType.URL) {
+ inSession = desktop.vamsasImport(new URL(vamsasImport));
+ }
+
+ } catch (Exception e) {
+ System.err.println("Exeption when importing " + vamsasImport + " as a vamsas document.");
+ e.printStackTrace();
+ }
+ if (!inSession) {
+ System.err.println("Failed to import " + vamsasImport + " as a vamsas document.");
+ } else {
+ System.out.println("Imported Successfully into new session "
+ + desktop.getVamsasApplication().getCurrentSession());
+ }
+ }
+ if (vamsasSession != null) {
+ if (vamsasImport != null) {
+ // close the newly imported session and import the Jalview specific
+ // remnants into the new session later on.
+ desktop.vamsasStop_actionPerformed(null);
+ }
+ // now join the new session
+ try {
+ if (desktop.joinVamsasSession(vamsasSession)) {
+ System.out.println("Successfully joined vamsas session " + vamsasSession);
+ } else {
+ System.err.println("WARNING: Failed to join vamsas session " + vamsasSession);
+ }
+ } catch (Exception e) {
+ System.err.println("ERROR: Failed to join vamsas session " + vamsasSession);
+ e.printStackTrace();
+ }
+ if (vamsasImport != null) {
+ // the Jalview specific remnants can now be imported into the new
+ // session at the user's leisure.
+ Cache.log.info("Skipping Push for import of data into existing vamsas session."); // TODO:
+ // enable
+ // this
+ // when
+ // debugged
+ // desktop.getVamsasApplication().push_update();
+ }
+ }
+ }
+ 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 && 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 = 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"
+ // +
+ // "-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 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;
+ }
}
-
-/**
- * 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;
- }
-};