*/
package jalview.bin;
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import 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.api.JalviewJSApp;
+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;
+//import netscape.javascript.JSObject;
/**
* 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
+public class Jalview implements ApplicationSingletonI
{
- /*
- * singleton instance of this class
- */
- private static Jalview instance;
+
+ // 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 static AlignFrame currentAlignFrame;
+ 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
{
- // grab all the rights we can the JVM
- Policy.setPolicy(new Policy()
+ if (Platform.isJS()) {
+ Platform.getURLCommandArguments();
+ } else /** @j2sIgnore */
{
- @Override
- public PermissionCollection getPermissions(CodeSource codesource)
+ // grab all the rights we can for the JVM
+ Policy.setPolicy(new Policy()
{
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
- @Override
- public void refresh()
- {
- }
- });
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
}
/**
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
*/
private int queued = 0;
}
- public static Jalview getInstance()
- {
- return instance;
- }
+ private final static boolean doPlatformLogging = false;
/**
* main class for Jalview application
*/
public static void main(String[] args)
{
- instance = new Jalview();
- instance.doMain(args);
+ if (doPlatformLogging)
+ {
+ Platform.startJavaLogging();
+ }
+ getInstance().doMain(args);
}
/**
*/
void doMain(String[] args)
{
- System.setSecurityManager(null);
+
+ boolean isJS = Platform.isJS();
+ if (!isJS)
+ {
+ 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"));
-
- ArgsParser aparser = new ArgsParser(args);
- boolean headless = false;
-
- if (aparser.contains("help") || aparser.contains("h"))
+ String val = System.getProperty("sys.install4jVersion");
+ if (val != null)
{
- showUsage();
- System.exit(0);
+ System.out.println("Install4j version: " + val);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+ val = System.getProperty("installer_template_version");
+ if (val != null)
{
- System.setProperty("java.awt.headless", "true");
- headless = true;
+ System.out.println("Install4j template version: " + val);
}
- String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
- if (usrPropsFile != null)
+ val = System.getProperty("launcher_version");
+ if (val != null)
{
- System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ System.out.println("Launcher version: " + val);
}
- // anything else!
+ // report Jalview version
+ Cache.getInstance().loadBuildProperties(true);
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ ArgsParser aparser = new ArgsParser(args);
+ headless = false;
+
+ String usrPropsFile = aparser.getValue("props");
+
+ Cache.loadProperties(usrPropsFile); // must do this before
+
+ if (isJS)
{
- try
+ 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)
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
System.out.println(
- "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
- } catch (MalformedURLException e)
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ }
+ if (aparser.contains("help") || aparser.contains("h"))
{
- System.err.println(
- "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ showUsage();
+ System.exit(0);
}
- }
+ // ?>>
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ // <<?
+
+ // anything else!
- String defs = aparser.getValue("setprop");
+ final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
+ if (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('=');
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));
+ if (isJS)
+ {
+ Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ }
}
defs = aparser.getValue("setprop");
}
{
error.printStackTrace();
System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
System.exit(0);
}
desktop = null;
- try
- {
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
- } catch (Exception ex)
+ if (!isJS)
+ /** @j2sIgnore */
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
- }
- if (Platform.isAMac())
- {
-
- LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel();
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
- if (lookAndFeel != null)
+ try
{
- try
- {
- UIManager.setLookAndFeel(lookAndFeel);
- } catch (Throwable e)
- {
- System.err.println(
- "Failed to set QuaQua look and feel: " + e.toString());
- }
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
}
- if (lookAndFeel == null || !(lookAndFeel.getClass()
- .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
- || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ if (Platform.isMac())
{
- try
+
+ 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)
{
- 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)
+ 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"))
{
- System.err.println(
- "Failed to reset look and feel: " + e.toString());
+ try
+ {
+ System.err.println(
+ "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+ UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to reset look and feel: " + e.toString());
+ }
}
}
}
-
/*
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
+ * 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
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ boolean soDefault = !isJS;
+ if (Cache.getDefault("USE_FULL_SO", soDefault))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
if (!headless)
{
- desktop = new Desktop();
+ desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
- desktop.setVisible(true);
- desktop.startServiceDiscovery();
- if (!aparser.contains("nousagestats"))
+ try
{
- startUsageStats(desktop);
- }
- else
+ JalviewTaskbar.setTaskbar(this);
+ } catch (Throwable t)
{
- System.err.println("CMD [-nousagestats] executed successfully!");
+ System.out.println("Error setting Taskbar: " + t.getMessage());
}
+ desktop.setVisible(true);
- if (!aparser.contains("noquestionnaire"))
+ if (!isJS)
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- String url = aparser.getValue("questionnaire");
- if (url != null)
+ desktop.startServiceDiscovery();
+ if (!aparser.contains("nousagestats"))
{
- // 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!");
+ startUsageStats(desktop);
}
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);
- }
+ System.err.println("CMD [-nousagestats] executed successfully!");
}
- }
- else
- {
- System.err.println("CMD [-noquestionnaire] executed successfully!");
- }
-
- if (!aparser.contains("nonews"))
- {
- desktop.checkForNews();
- }
-
- BioJsHTMLOutput.updateBioJS();
- }
- String file = null, data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- FileLoader fileLoader = new FileLoader(!headless);
- Vector<String> 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");
- String vamsasSession = aparser.getValue("vsess");
- if (vamsasImport != null || vamsasSession != null)
- {
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- if (vamsasImport != null)
- {
- try
+ if (!aparser.contains("noquestionnaire"))
{
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
{
- inSession = desktop.vamsasImport(new File(vamsasImport));
+ // 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 (viprotocol == DataSourceType.URL)
+ else
{
- inSession = desktop.vamsasImport(new URL(vamsasImport));
+ 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);
+ }
}
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
}
- if (!inSession)
+ else
{
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
+ System.err
+ .println("CMD [-noquestionnaire] executed successfully!");
}
- else
+
+ if (!aparser.contains("nonews"))
{
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
+ desktop.checkForNews();
}
+
+ BioJsHTMLOutput.updateBioJS();
}
- if (vamsasSession != null)
+ }
+ 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)
{
- 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
+ final File appdir = new File(appdirString);
+ new Thread()
{
- if (desktop.joinVamsasSession(vamsasSession))
+ @Override
+ public void run()
{
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
}
- 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();
- }
+ }.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);
+ }
+
+ // 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.
+ JalviewJSApp jsApp = null;
+ AlignFrame af = null;
+
if (file != null)
{
if (!headless)
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
- if (!(new File(file)).exists())
+ if (!file.startsWith("http://") && !file.startsWith("https://"))
+ // BH 2019 added https check for Java
{
- System.out.println("Can't find " + file);
- if (headless)
+ if (!(new File(file)).exists())
{
- System.exit(1);
+ 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 = new IdentifyFile().identify(file, protocol);
+ format = (fileFormat != null
+ ? FileFormats.getInstance().forName(fileFormat)
+ : null);
+ if (format == null)
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
} catch (FileFormatException e1)
{
// TODO ?
}
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ 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!");
+ }
+
+ af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
format);
if (af == null)
{
}
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);
- data = aparser.getValue("colour", true);
+
+ String data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
if (cs != null)
{
}
// Must maintain ability to use the groups flag
- data = aparser.getValue("groups", true);
+ data = aparser.getValue(ArgsParser.GROUPS, true);
if (data != null)
{
af.parseFeaturesFile(data,
System.out.println(
"CMD groups[-" + data + "] executed successfully!");
}
- data = aparser.getValue("features", true);
+ data = aparser.getValue(ArgsParser.FEATURES, true);
if (data != null)
{
af.parseFeaturesFile(data,
System.out.println(
"CMD [-features " + data + "] executed successfully!");
}
-
- data = aparser.getValue("annotations", true);
+ data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
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("sortbytree"))
+ if (aparser.contains(ArgsParser.SORTBYTREE))
{
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
- if (aparser.contains("no-annotation"))
+
+ boolean doUpdateAnnotation = false;
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
{
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
{
- System.out.println("CMD no-annotation executed successfully!");
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD no-annotation executed successfully!");
+ }
}
}
- if (aparser.contains("nosortbytree"))
+
+ if (aparser.contains(ArgsParser.NOSORTBYTREE))
{
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
+ doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
- data = aparser.getValue("tree", true);
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
+
+ data = aparser.getValue(ArgsParser.TREE, true);
if (data != null)
{
try
{
- System.out.println(
- "CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
af.getViewport()
.setCurrentTree(af.showNewickTree(nf, data).getTree());
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
// (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)
+ if (isJS)
{
- // 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;
+ jsApp = new JalviewJSApp(this, aparser);
+ jsApp.load(af);
}
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
-
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
- {
- System.err.println("The output html file must not be null");
- return;
- }
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out
- .println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
-
- if (af.saveAlignment(file, format))
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
- }
- else
+ if (groovyscript != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ // 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;
}
-
- }
-
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ createOutputFiles(aparser, af, format);
}
}
}
- 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))
+ else
{
- 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"))
+ if (!isJS && !headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- // hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
- // and remove the stale setting
- jalview.bin.Cache.removeProperty("STARTUP_FILE");
- }
- protocol = DataSourceType.FILE;
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ // ////////////////////
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ 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");
+ }
- if (file.endsWith(".jar"))
- {
- format = FileFormat.Jalview;
- }
- else
- {
- try
+ protocol = DataSourceType.FILE;
+
+ if (file.indexOf("http:") > -1)
{
- format = new IdentifyFile().identify(file, protocol);
- } catch (FileFormatException e)
+ protocol = DataSourceType.URL;
+ }
+
+ if (file.endsWith(".jar"))
{
- // TODO what?
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ 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);
+ af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+
}
}
+ // extract groovy arguments before anything else.
// Once all other stuff is done, execute any groovy scripts (in order)
- if (groovyscript != null)
+ if (!isJS && groovyscript != null)
{
if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, startUpAlframe);
+ executeGroovyScript(groovyscript, af);
}
else
{
+ groovyscript);
}
}
+
// and finally, turn off batch mode indicator - if the desktop still exists
if (desktop != null)
{
}
desktop.setInBatchMode(false);
}
+
+ if (isJS && isStartup)
+ {
+ jsApp.callInitCallback();
+ }
+ }
+
+
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ * <ul>
+ * <li>png</li>
+ * <li>svg</li>
+ * <li>html</li>
+ * <li>biojsmsa</li>
+ * <li>imgMap</li>
+ * <li>eps</li>
+ * </ul>
+ * 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 af
+ * @param format
+ */
+ private void createOutputFiles(ArgsParser aparser, AlignFrame af,
+ FileFormatI format)
+ {
+ 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;
+ }
+ if (!Platform.isJS()) /** @j2sIgnore */
+ {
+ // skipping outputFormat?
+ System.out.println("Unknown arg: " + outputFormat);
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ af.saveAlignment(fname, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println(
+ "Written alignment in " + format + " format to " + fname);
+ }
+ else
+ {
+ System.out.println("Error writing file " + fname + " in " + format
+ + " format!!");
+ }
+ }
+ break;
+ }
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
}
private static void showUsage()
// (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");
}
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+ 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 ?"
}
try
{
- Map<String, Object> vbinding = new HashMap<>();
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
}
}
- /**
- * Check commandline for any das server definitions or any fetchfrom switches
- *
- * @return vector of DAS source nicknames to retrieve from
- */
- private static Vector<String> checkDasArguments(ArgsParser aparser)
- {
- Vector<String> 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;
- 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 FeatureFetcher startFeatureFetching(
- final Vector<String> 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()
{
String isheadless = System.getProperty("java.awt.headless");
public static AlignFrame getCurrentAlignFrame()
{
- return Jalview.currentAlignFrame;
+ return Jalview.getInstance().currentAlignFrame;
}
public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- Jalview.currentAlignFrame = currentAlignFrame;
+ Jalview.getInstance().currentAlignFrame = currentAlignFrame;
+ }
+
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
}
+
}
git://source.jalview.org / jalview.git / blobdiff