/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
*/
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.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
*
* 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 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);
}
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();
}
}
}
// Finally, deal with the remaining input data.
if (file != null)
{
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",
"http://www.jalview.org/examples/exampleFile_2_3.jar");
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)
{
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.");
}
File sfile = null;
if (groovyscript.trim().equals("STDIN"))
{
// read from stdin into a tempfile and execute it
try
{
sfile = File.createTempFile("jalview", "groovy");
PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(sfile)));
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 "
+ ((sfile == null) ? "(tempfile wasn't created)" : sfile
.toString()));
ex.printStackTrace();
return;
}
}
else
{
sfile = new File(groovyscript);
}
if (!sfile.exists())
{
System.err.println("File '" + groovyscript + "' does not exist.");
return;
}
if (!sfile.canRead())
{
System.err.println("File '" + groovyscript + "' cannot be read.");
return;
}
if (sfile.length() < 1)
{
System.err.println("File '" + groovyscript + "' is empty.");
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;
for (int jc=0;jc 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;
}
};