/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*/
package jalview.bin;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.HtmlSvgOutput;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
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.util.Vector;
import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
+import javax.swing.UIManager.LookAndFeelInfo;
+
+import com.threerings.getdown.util.LaunchUtil;
+
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+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.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.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
/**
* Main class for Jalview Application <br>
* <br>
- * 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
{
+ /*
+ * 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();
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<String> 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
*/
public static void main(String[] args)
{
- System.out.println("Java version: "
- + System.getProperty("java.version"));
+ 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("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.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
Cache.loadProperties(usrPropsFile); // must do this before
if (usrPropsFile != null)
{
- System.out.println("CMD [-props " + usrPropsFile
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
}
// anything else!
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println("CMD [-jabaws " + jabawsUrl
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
{
- System.err.println("Invalid jabaws parameter: " + jabawsUrl
- + " ignored");
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
}
}
try
{
Cache.initLogger();
- } catch (java.lang.NoClassDefFoundError error)
+ } catch (NoClassDefFoundError error)
{
error.printStackTrace();
- System.out
- .println("\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
System.exit(0);
}
- Desktop desktop = null;
+ desktop = null;
- try
- {
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
- } catch (Exception ex)
+ setLookAndFeel();
+
+ /*
+ * configure 'full' SO model if preferences say to, else use the default (SO
+ * Lite)
+ */
+ if (Cache.getDefault("USE_FULL_SO", true))
{
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
}
- if (new Platform().isAMac())
+
+ if (!headless)
{
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
+
+ desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
+
try
{
- UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel());
- } catch (UnsupportedLookAndFeelException e)
+ JalviewTaskbar.setTaskbar(this);
+ } catch (Exception e)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ Cache.log.info("Cannot set Taskbar");
+ Cache.log.error(e.getMessage());
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ Cache.log.info("Cannot set Taskbar");
+ Cache.log.error(t.getMessage());
+ // t.printStackTrace();
}
- }
- if (!headless)
- {
- desktop = new Desktop();
- desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
- System.out.println("CMD questionnaire[-" + url
- + "] executed successfully!");
+ System.out.println(
+ "CMD questionnaire[-" + url + "] executed successfully!");
}
else
{
// 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);
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug(
+ "Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
{
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
- desktop.checkForNews();
+
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
+ {
+ desktop.checkForNews();
+ }
+
+ BioJsHTMLOutput.updateBioJS();
}
- if (!isHeadlessMode())
+ // 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)
{
- BioJsHTMLOutput.updateBioJS();
+ 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, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
- Vector getFeatures = null; // vector of das source nicknames to fetch
- // features from
- // loading is done.
+ 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
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(MessageManager
- .getString("status.processing_commandline_args"),
+ desktop.setProgressBar(
+ MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ protocol = AppletFormatAdapter.checkProtocol(file);
+
+ if (protocol == DataSourceType.FILE)
{
- if (!(new java.io.File(file)).exists())
+ if (!(new File(file)).exists())
{
System.out.println("Can't find " + file);
if (headless)
}
}
- protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
-
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
}
else
{
- Desktop.setCurrentAlignFrame(af);
+ setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
- if (cs == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
- else
+ if (cs != null)
{
- System.out.println("CMD [-color " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
}
af.changeColour(cs);
}
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
- System.out.println("CMD groups[-" + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
- System.out.println("CMD [-features " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
{
af.loadJalviewDataFile(data, null, null, null);
// System.out.println("Added " + data);
- System.out.println("CMD [-annotations " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
data = aparser.getValue("tree", true);
if (data != null)
{
- jalview.io.NewickFile fin = null;
try
{
- System.out.println("CMD [-tree " + data
- + "] executed successfully!");
- 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(
+ "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);
// 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 });
-
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- }
- else
- {
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
- }
+ 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)
{
- format = aparser.nextValue();
+ String outputFormat = aparser.nextValue();
file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ if (outputFormat.equalsIgnoreCase("png"))
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
System.out.println("Creating PNG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("svg"))
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
System.out.println("Creating SVG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("html"))
+ else if (outputFormat.equalsIgnoreCase("html"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
- new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
System.out.println("Creating HTML image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("imgMap"))
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
{
- af.createImageMap(new java.io.File(file), imageName);
+ 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 (format.equalsIgnoreCase("eps"))
+ else if (outputFormat.equalsIgnoreCase("eps"))
{
- File outputFile = new java.io.File(file);
- System.out.println("Creating EPS file: "
- + outputFile.getAbsolutePath());
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
af.createEPS(outputFile);
continue;
}
-
- if (af.saveAlignment(file, format))
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
- else
+ if (outFormat != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ }
+ else
+ {
+ if (af.saveAlignment(file, outFormat))
+ {
+ 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)
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
+ if (!headless && file == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
- file = jalview.bin.Cache.getDefault(
- "STARTUP_FILE",
+ 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"))
+ "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
- protocol = "File";
-
- if (file.indexOf("http:") > -1)
- {
- protocol = "URL";
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
}
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())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] { desktop,
- startUpAlframe });
+ executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ System.err.println(
+ "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ groovyscript);
}
}
}
}
+ private static void setLookAndFeel()
+ {
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
+ // "mac"
+ // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
+ // try Quaqua/Vaqua.
+ String lafProp = System.getProperty("laf");
+ String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+ String laf = "none";
+ if (lafProp != null)
+ {
+ laf = lafProp;
+ }
+ else if (lafSetting != null)
+ {
+ laf = lafSetting;
+ }
+ boolean lafSet = false;
+ switch (laf)
+ {
+ case "crossplatform":
+ lafSet = setCrossPlatformLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "system":
+ lafSet = setSystemLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "gtk":
+ lafSet = setGtkLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "metal":
+ lafSet = setMetalLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "nimbus":
+ lafSet = setNimbusLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "quaqua":
+ lafSet = setQuaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "vaqua":
+ lafSet = setVaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "mac":
+ lafSet = setMacLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "none":
+ break;
+ default:
+ Cache.log.error("Requested laf=" + laf + " not implemented");
+ }
+ if (!lafSet)
+ {
+ setSystemLookAndFeel();
+ if (Platform.isLinux())
+ {
+ setMetalLookAndFeel();
+ }
+ if (Platform.isAMac())
+ {
+ setMacLookAndFeel();
+ }
+ }
+ }
+
+ private static boolean setCrossPlatformLookAndFeel()
+ {
+ return setGenericLookAndFeel(false);
+ }
+
+ private static boolean setSystemLookAndFeel()
+ {
+ return setGenericLookAndFeel(true);
+ }
+
+ private static boolean setGenericLookAndFeel(boolean system)
+ {
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(
+ system ? UIManager.getSystemLookAndFeelClassName()
+ : UIManager.getCrossPlatformLookAndFeelClassName());
+ set = true;
+ } catch (Exception ex)
+ {
+ Cache.log.error("Unexpected Look and Feel Exception");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
+ }
+ return set;
+ }
+
+ private static boolean setSpecificLookAndFeel(String name,
+ String className, boolean nameStartsWith)
+ {
+ boolean set = false;
+ try
+ {
+ for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
+ {
+ if (info.getName() != null && nameStartsWith
+ ? info.getName().toLowerCase()
+ .startsWith(name.toLowerCase())
+ : info.getName().toLowerCase().equals(name.toLowerCase()))
+ {
+ className = info.getClassName();
+ break;
+ }
+ }
+ UIManager.setLookAndFeel(className);
+ set = true;
+ } catch (Exception ex)
+ {
+ Cache.log.error("Unexpected Look and Feel Exception");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
+ }
+ return set;
+ }
+
+ private static boolean setGtkLookAndFeel()
+ {
+ return setSpecificLookAndFeel("gtk",
+ "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
+ }
+
+ private static boolean setMetalLookAndFeel()
+ {
+ return setSpecificLookAndFeel("metal",
+ "javax.swing.plaf.metal.MetalLookAndFeel", false);
+ }
+
+ private static boolean setNimbusLookAndFeel()
+ {
+ return setSpecificLookAndFeel("nimbus",
+ "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
+ }
+
+ private static boolean setQuaquaLookAndFeel()
+ {
+ return setSpecificLookAndFeel("quaqua",
+ ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
+ .getName(),
+ false);
+ }
+
+ private static boolean setVaquaLookAndFeel()
+ {
+ return setSpecificLookAndFeel("vaqua",
+ "org.violetlib.aqua.AquaLookAndFeel", false);
+ }
+
+ private static boolean setMacLookAndFeel()
+ {
+ boolean set = false;
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ set = setQuaquaLookAndFeel();
+ if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
+ .toLowerCase().contains("quaqua"))
+ {
+ set = setVaquaLookAndFeel();
+ }
+ return set;
+ }
+
private static void showUsage()
{
- System.out
- .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ 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"
+ "-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)"
+ // "-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"
- + "-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");
+ + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ + "\n~Read documentation in Application or visit https://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.
*/
- jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
- desktop.desktop,
- "USAGESTATS",
- "Jalview 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.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.");
* the Jalview Desktop object passed in to the groovy binding as the
* 'Jalview' object.
*/
- private static void executeGroovyScript(String groovyscript,
- Object[] jalviewContext)
+ private void executeGroovyScript(String groovyscript, AlignFrame af)
{
- 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
*/
try
{
tfile = File.createTempFile("jalview", "groovy");
- PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(tfile)));
+ PrintWriter outfile = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(tfile)));
BufferedReader br = new BufferedReader(
- new java.io.InputStreamReader(System.in));
+ new InputStreamReader(System.in));
String line = null;
while ((line = br.readLine()) != null)
{
} catch (Exception ex)
{
System.err.println("Failed to read from STDIN into tempfile "
- + ((tfile == null) ? "(tempfile wasn't created)" : tfile
- .toString()));
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
ex.printStackTrace();
return;
}
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err
- .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ System.err.println(
+ "Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ tfile.toURI());
x.printStackTrace();
return;
}
}
}
- boolean success = false;
try
{
- /*
- * The following code performs the GroovyScriptEngine invocation using
- * reflection, and is equivalent to this fragment from the embedding
- * groovy documentation on the groovy site: <code> import
- * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
- *
- * String[] roots = new String[] { "/my/groovy/script/path" };
- * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
- * = new Binding(); binding.setVariable("input", "world");
- * gse.run("hello.groovy", binding); </code>
- */
- Class<?>[] bspec;
- Object[] binding;
- int blen = ((jalviewContext[0] == null) ? 0 : 1)
- + ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[] { "Jalview", "currentAlFrame" };
- bspec = new Class[blen * 2];
- binding = new Object[blen * 2];
- blen = 0;
- ClassLoader cl = null;
- Map<String, Object> vbinding = new HashMap<String, Object>();
- for (int jc = 0; jc < jalviewContext.length; jc++)
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
+ vbinding.put("Jalview", this);
+ if (af != null)
{
- 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++;
- }
+ vbinding.put("currentAlFrame", af);
}
- Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor<?> gbcons;
- Object gbinding;
- try
- {
- gbcons = gbindingc.getConstructor(Map.class);
- gbinding = gbcons.newInstance(vbinding);
- } catch (NoSuchMethodException x)
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
{
- // old style binding config - using series of string/object values to
- // setVariable.
- gbcons = gbindingc.getConstructor();
- gbinding = gbcons.newInstance();
- java.lang.reflect.Method setvar = gbindingc.getMethod(
- "setVariable", bspec);
- setvar.invoke(gbinding, binding);
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
}
-
- 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
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);
- }
- System.out.println("CMD [-dasserver " + data
- + "] executed successfully!");
- } // 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;
}
public static boolean isHeadlessMode()
}
return false;
}
-}
-
-/**
- * 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 rnabuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
- {
- System.out.println("Good idea ! ");
-
- }
-}
-class pbuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
+ public AlignFrame[] getAlignFrames()
{
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
}
-}
-
-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.
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
- public String getValue(String arg)
- {
- return getValue(arg, false);
- }
-
- public String getValue(String arg, boolean utf8decode)
+ public void quit()
{
- 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))
+ if (desktop != null)
{
- vargs.removeElement(arg);
- return true;
+ desktop.quit();
}
else
{
- return false;
+ System.exit(0);
}
}
- public String nextValue()
+ public static AlignFrame getCurrentAlignFrame()
{
- return vargs.remove(0).toString();
+ return Jalview.currentAlignFrame;
}
- public int getSize()
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- return vargs.size();
+ 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(MessageManager
- .getString("status.das_features_being_retrived"), id);
- af.featureSettings_actionPerformed(null);
- af.featureSettings.fetchDasFeatures(dasSources, true);
- af.setProgressBar(null, id);
- synchronized (us)
- {
- running--;
- }
- }
- }).start();
- }
-
- public synchronized boolean allFinished()
- {
- return queued == 0 && running == 0;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff