/*
* 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 java.awt.GraphicsEnvironment;
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;
import jalview.api.AlignCalcWorkerI;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
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.FileFormats;
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;
/**
* 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 implements ApplicationSingletonI
{
// for testing those nasty messages you cannot ever find.
// static
// {
// System.setOut(new PrintStream(new ByteArrayOutputStream())
// {
// @Override
// public void println(Object o)
// {
// if (o != null)
// {
// System.err.println(o);
// }
// }
//
// });
// }
public static Jalview getInstance()
{
return (Jalview) ApplicationSingletonProvider
.getInstance(Jalview.class);
}
private Jalview()
{
}
private boolean headless;
private Desktop desktop;
public AlignFrame currentAlignFrame;
public String appletResourcePath;
public String j2sAppletID;
private boolean noCalculation, noMenuBar, noStatus;
private boolean noAnnotation;
public boolean getStartCalculations()
{
return !noCalculation;
}
public boolean getAllowMenuBar()
{
return !noMenuBar;
}
public boolean getShowStatus()
{
return !noStatus;
}
public boolean getShowAnnotation()
{
return !noAnnotation;
}
static
{
if (Platform.isJS()) {
Platform.getURLCommandArguments();
} else /** @j2sIgnore */
{
// grab all the rights we can for 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;
}
}
private final static boolean doPlatformLogging = false;
/**
* main class for Jalview application
*
* @param args
* open filename
*/
public static void main(String[] args)
{
if (doPlatformLogging)
{
Platform.startJavaLogging();
}
getInstance().doMain(args);
}
/**
* @param args
*/
void doMain(String[] args)
{
boolean isJS = Platform.isJS();
if (!isJS)
{
System.setSecurityManager(null);
}
/*
* @j2sNative J2S.db._DirectDatabaseCalls["compbio.dundee.ac.uk"]=null;
* @j2sNative J2S.db._DirectDatabaseCalls["jalview.org"]=null;
*
*/
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
System.out.println("Install4j version: " + val);
}
val = System.getProperty("installer_template_version");
if (val != null)
{
System.out.println("Install4j template version: " + val);
}
val = System.getProperty("launcher_version");
if (val != null)
{
System.out.println("Launcher version: " + val);
}
// report Jalview version
Cache.getInstance().loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
headless = false;
String usrPropsFile = aparser.getValue("props");
Cache.loadProperties(usrPropsFile); // must do this before
boolean allowServices = true;
if (isJS)
{
j2sAppletID = Platform.getAppID(null);
Preferences.setAppletDefaults();
Cache.loadProperties(usrPropsFile); // again, because we
// might be changing defaults here?
appletResourcePath = (String) aparser.getAppletValue("resourcepath",
null, true);
}
else
/**
* Java only
*
* @j2sIgnore
*/
{
if (usrPropsFile != null)
{
System.out.println(
"CMD [-props " + usrPropsFile + "] executed successfully!");
}
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
System.exit(0);
}
// BH note: Only -nodisplay is official; others are deprecated?
if (aparser.contains("nodisplay") || aparser.contains("nogui")
|| aparser.contains("headless")
|| GraphicsEnvironment.isHeadless())
{
if (!isJS) {
// BH Definitely not a good idea in JavaScript;
// probably should not be here for Java, either.
System.setProperty("java.awt.headless", "true");
}
headless = true;
}
final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
allowServices = !("none".equals(jabawsUrl));
if (allowServices && jabawsUrl != null)
{
try
{
Jws2Discoverer.getInstance().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(ArgsParser.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);
if (isJS)
{
Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
}
defs = aparser.getValue("setprop");
}
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);
}
if (!isJS)
/** @j2sIgnore */
{
try
{
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception ex)
{
System.err.println("Unexpected Look and Feel Exception");
ex.printStackTrace();
}
if (Platform.isMac())
{
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 (full SO)
* - as JS currently doesn't have OBO parsing, it must use 'Lite' version
*/
boolean soDefault = !isJS;
if (Cache.getDefault("USE_FULL_SO", soDefault))
{
SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
desktop = null;
if (!headless)
{
desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
try
{
JalviewTaskbar.setTaskbar(this);
} catch (Throwable t)
{
System.out.println("Error setting Taskbar: " + t.getMessage());
}
desktop.setVisible(true);
if (Platform.isJS())
Cache.setProperty("SHOW_JWS2_SERVICES", "false");
if (allowServices)
{
desktop.startServiceDiscovery();
}
if (!isJS)
/**
* Java only
*
* @j2sIgnore
*/
{
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();
}
}
parseArguments(aparser, true);
}
/**
* Parse all command-line String[] arguments as well as all JavaScript-derived
* parameters from Info.
*
* We allow for this method to be run from JavaScript. Basically allowing
* simple scripting.
*
* @param aparser
* @param isStartup
*/
public void parseArguments(ArgsParser aparser, boolean isStartup)
{
String groovyscript = null; // script to execute after all loading is
boolean isJS = Platform.isJS();
if (!isJS)
/** @j2sIgnore */
{
// 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();
}
// completed one way or another
// extract groovy argument and execute if necessary
groovyscript = aparser.getValue("groovy", true);
}
String file = aparser.getValue("open", true);
if (!isJS && file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
setDisplayParameters(aparser);
// time to open a file.
long progress = -1;
DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
FileFormatI format = null;
// Finally, deal with the remaining input data.
AlignFrame af = null;
JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);
if (file == null)
{
if (isJS)
{
// JalviewJS allows sequence1 sequence2 ....
}
else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
*
* @j2sIgnore
*/
{
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
file = Cache.getDefault("STARTUP_FILE",
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
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?
}
}
af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
}
}
else
{
if (!headless)
{
desktop.setProgressBar(
MessageManager
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
System.out.println("CMD [-open " + file + "] executed successfully!");
if (!Platform.isJS())
/**
* ignore in JavaScript -- can't just file existence - could load it?
*
* @j2sIgnore
*/
{
if (!file.startsWith("http://") && !file.startsWith("https://"))
// BH 2019 added https check for Java
{
if (!(new File(file)).exists())
{
System.out.println("Can't find " + file);
if (headless)
{
System.exit(1);
}
}
}
}
String fileFormat = (isJS
? (String) aparser.getAppletValue("format", null, true)
: null);
protocol = AppletFormatAdapter.checkProtocol(file);
try
{
format = (fileFormat != null
? FileFormats.getInstance().forName(fileFormat)
: null);
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
}
} catch (FileFormatException e1)
{
// TODO ?
}
af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
format);
if (af == null)
{
System.out.println("jalview error - AlignFrame was not created");
}
else
{
// JalviewLite interface for JavaScript allows second file open
String file2 = aparser.getValue(ArgsParser.OPEN2, true);
if (file2 != null)
{
protocol = AppletFormatAdapter.checkProtocol(file2);
try
{
format = new IdentifyFile().identify(file2, protocol);
} catch (FileFormatException e1)
{
// TODO ?
}
AlignFrame af2 = new FileLoader(!headless)
.LoadFileWaitTillLoaded(file2, protocol, format);
if (af2 == null)
{
System.out.println("error");
}
else
{
AlignViewport.openLinkedAlignmentAs(af,
af.getViewport().getAlignment(),
af2.getViewport().getAlignment(), "",
AlignViewport.SPLIT_FRAME);
System.out.println(
"CMD [-open2 " + file2 + "] executed successfully!");
}
}
setCurrentAlignFrame(af);
setFrameDependentProperties(aparser, af);
if (isJS)
{
jsApp.initFromParams(af);
}
else
/**
* Java only
*
* @j2sIgnore
*/
{
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;
}
}
if (!isJS || !isStartup) {
createOutputFiles(aparser, format);
}
}
if (headless)
{
af.getViewport().getCalcManager().shutdown();
}
}
// extract groovy arguments before anything else.
// Once all other stuff is done, execute any groovy scripts (in order)
if (!isJS && groovyscript != null)
{
if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, af);
}
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);
}
if (jsApp != null) {
jsApp.callInitCallback();
}
}
/**
* Set general display parameters irrespective of file loading or headlessness.
*
* @param aparser
*/
private void setDisplayParameters(ArgsParser aparser)
{
if (aparser.contains(ArgsParser.NOMENUBAR))
{
noMenuBar = true;
System.out.println("CMD [nomenu] executed successfully!");
}
if (aparser.contains(ArgsParser.NOSTATUS))
{
noStatus = true;
System.out.println("CMD [nostatus] executed successfully!");
}
if (aparser.contains(ArgsParser.NOANNOTATION)
|| aparser.contains(ArgsParser.NOANNOTATION2))
{
noAnnotation = true;
System.out.println("CMD no-annotation executed successfully!");
}
if (aparser.contains(ArgsParser.NOCALCULATION))
{
noCalculation = true;
System.out.println("CMD [nocalculation] executed successfully!");
}
}
private void setFrameDependentProperties(ArgsParser aparser,
AlignFrame af)
{
String data = aparser.getValue(ArgsParser.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(ArgsParser.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(ArgsParser.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(ArgsParser.ANNOTATIONS, true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
// System.out.println("Added " + data);
System.out.println(
"CMD [-annotations " + data + "] executed successfully!");
}
// JavaScript feature
if (aparser.contains(ArgsParser.SHOWOVERVIEW))
{
af.overviewMenuItem_actionPerformed(null);
System.out.println("CMD [showoverview] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains(ArgsParser.SORTBYTREE))
{
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
{
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
boolean doUpdateAnnotation = false;
/**
* we do this earlier in JalviewJS because of a complication with
* SHOWOVERVIEW
*
* For now, just fixing this in JalviewJS.
*
*
* @j2sIgnore
*
*/
{
if (noAnnotation)
{
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
doUpdateAnnotation = true;
}
}
}
if (aparser.contains(ArgsParser.NOSORTBYTREE))
{
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
if (doUpdateAnnotation)
{ // BH 2019.07.24
af.setMenusForViewport();
af.alignPanel.updateLayout();
}
data = aparser.getValue(ArgsParser.TREE, true);
if (data != null)
{
try
{
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
af.getViewport()
.setCurrentTree(af.showNewickTree(nf, data).getTree());
System.out.println(
"CMD [-tree " + data + "] executed successfully!");
} 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)
}
/**
* Writes an output file for each format (if any) specified in the
* command-line arguments. Supported formats are currently
*
* - png
* - svg
* - html
* - biojsmsa
* - imgMap
* - eps
*
* A format parameter should be followed by a parameter specifying the output
* file name. {@code imgMap} parameters should follow those for the
* corresponding alignment image output.
*
* @param aparser
* @param format
*/
private void createOutputFiles(ArgsParser aparser, FileFormatI format)
{
AlignFrame af = currentAlignFrame;
while (aparser.getSize() >= 2)
{
String outputFormat = aparser.nextValue();
File imageFile;
String fname;
switch (outputFormat.toLowerCase())
{
case "png":
imageFile = new File(aparser.nextValue());
af.createPNG(imageFile);
System.out.println(
"Creating PNG image: " + imageFile.getAbsolutePath());
continue;
case "svg":
imageFile = new File(aparser.nextValue());
af.createSVG(imageFile);
System.out.println(
"Creating SVG image: " + imageFile.getAbsolutePath());
continue;
case "eps":
imageFile = new File(aparser.nextValue());
System.out.println(
"Creating EPS file: " + imageFile.getAbsolutePath());
af.createEPS(imageFile);
continue;
case "biojsmsa":
fname = new File(aparser.nextValue()).getAbsolutePath();
try
{
BioJsHTMLOutput.refreshVersionInfo(
BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
} catch (URISyntaxException e)
{
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
bjs.exportHTML(fname);
System.out.println("Creating BioJS MSA Viwer HTML file: " + fname);
continue;
case "html":
fname = new File(aparser.nextValue()).getAbsolutePath();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
htmlSVG.exportHTML(fname);
System.out.println("Creating HTML image: " + fname);
continue;
case "imgmap":
imageFile = new File(aparser.nextValue());
af.alignPanel.makePNGImageMap(imageFile, "unnamed.png");
System.out.println(
"Creating image map: " + imageFile.getAbsolutePath());
continue;
default:
// fall through - try to parse as an alignment data export format
FileFormatI outFormat = null;
try
{
outFormat = FileFormats.getInstance().forName(outputFormat);
} catch (Exception formatP)
{
}
if (outFormat == null)
{
System.out.println("Couldn't parse " + outputFormat
+ " as a valid Jalview format string.");
continue;
}
if (!outFormat.isWritable())
{
System.out.println(
"This version of Jalview does not support alignment export as "
+ outputFormat);
continue;
}
// record file as it was passed to Jalview so it is recognisable to the CLI
// caller
String file;
fname = new File(file = aparser.nextValue()).getAbsolutePath();
// JBPNote - yuck - really wish we did have a bean returned from this which gave
// success/fail like before !
af.saveAlignment(fname, outFormat);
if (!af.isSaveAlignmentSuccessful())
{
System.out.println("Written alignment in " + outputFormat
+ " format to " + file);
continue;
}
else
{
System.out.println("Error writing file " + file + " in "
+ outputFormat + " format!!");
}
}
}
// ??? Should report - 'ignoring' extra args here...
while (aparser.getSize() > 0)
{
System.out.println("Ignoring extra argument: " + aparser.nextValue());
}
}
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.getDesktopPane(),
"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.getInstance().currentAlignFrame;
}
public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
Jalview.getInstance().currentAlignFrame = currentAlignFrame;
}
public void notifyWorker(AlignCalcWorkerI worker, String status)
{
// System.out.println("Jalview worker " + worker.getClass().getSimpleName()
// + " " + status);
}
private static boolean isInteractive = true;
public static boolean isInteractive()
{
return isInteractive;
}
public static void setInteractive(boolean tf)
{
isInteractive = tf;
}
}