X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3bc92ec381c65143df4418a1d78e5738497c79a2;hb=e32a5ade6bf19aca615f33b4664bbb6bcf4d2529;hp=164ba27c5209ad830e872290acd2b9ee3d984bed;hpb=fdeeb42848df5648feab5acc978a44e667785a1e;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 164ba27..3bc92ec 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,28 +20,6 @@
*/
package jalview.bin;
-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.FileLoader;
-import jalview.io.FormatAdapter;
-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.schemes.UserColourScheme;
-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;
@@ -51,6 +29,7 @@ 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;
@@ -60,19 +39,61 @@ import java.security.Policy;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import javax.swing.UIManager;
+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.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
*
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ *
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ *
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
*
* @author $author$
* @version $Revision$
*/
public class Jalview
{
+ static
+ {
+ Platform.getURLCommandArguments();
+ }
+
/*
* singleton instance of this class
*/
@@ -84,22 +105,30 @@ public class Jalview
static
{
- // grab all the rights we can the JVM
- Policy.setPolicy(new Policy()
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @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()
+ {
+ }
+ });
+ }
}
/**
@@ -111,8 +140,8 @@ public class Jalview
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;
@@ -145,7 +174,6 @@ public class Jalview
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)
{
@@ -175,21 +203,86 @@ public class Jalview
*/
public static void main(String[] args)
{
+ // setLogging(); // BH - for event debugging in JavaScript
instance = new Jalview();
instance.doMain(args);
}
+ private static void logClass(String name)
+ {
+ // BH - for event debugging in JavaScript
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ Logger logger = Logger.getLogger(name);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+
+ @SuppressWarnings("unused")
+ private static void setLogging()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
+ }
+
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Logger.getLogger("").setLevel(Level.ALL);
+ logClass("java.awt.EventDispatchThread");
+ logClass("java.awt.EventQueue");
+ logClass("java.awt.Component");
+ logClass("java.awt.focus.Component");
+ logClass("java.awt.focus.DefaultKeyboardFocusManager");
+ }
+
+ }
+
/**
* @param args
*/
void doMain(String[] args)
{
- System.setSecurityManager(null);
- System.out.println("Java version: "
- + System.getProperty("java.version"));
+
+ if (!Platform.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"));
+ 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;
@@ -209,24 +302,43 @@ public class Jalview
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!
-
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- try
+ if (aparser.contains("help") || aparser.contains("h"))
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println("CMD [-jabaws " + jabawsUrl
- + "] executed successfully!");
- } catch (MalformedURLException e)
+ showUsage();
+ System.exit(0);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
- System.err.println("Invalid jabaws parameter: " + jabawsUrl
- + " ignored");
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ // anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ }
}
}
@@ -241,6 +353,10 @@ public class Jalview
else
{
System.out.println("Executing setprop argument: " + defs);
+ if (Platform.isJS())
+ {
+ Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ }
// 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));
@@ -260,41 +376,21 @@ public class Jalview
} 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 = null;
- try
- {
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
- } catch (Exception ex)
- {
- }
- if (Platform.isAMac())
- {
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
- try
- {
- UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel());
- } catch (Throwable e)
- {
- System.err.println("Failed to set QuaQua look and feel: "
- + e.toString());
- }
- }
+ setLookAndFeel();
/*
- * 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 = !Platform.isJS();
+ if (Cache.getDefault("USE_FULL_SO", soDefault))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
@@ -303,64 +399,111 @@ public class Jalview
{
desktop = new Desktop();
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 (Exception e)
{
- System.err.println("CMD [-nousagestats] executed successfully!");
+ 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 (!aparser.contains("noquestionnaire"))
+ // set Proxy settings before all the internet calls
+ Cache.setProxyPropertiesFromPreferences();
+
+ desktop.setVisible(true);
+
+ if (!Platform.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)
+ 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
- // 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);
+ 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!");
- }
+ else
+ {
+ System.err
+ .println("CMD [-noquestionnaire] executed successfully!");
+ }
- if (!aparser.contains("nonews"))
- {
- desktop.checkForNews();
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
+ }
+
+ BioJsHTMLOutput.updateBioJS();
}
+ }
- BioJsHTMLOutput.updateBioJS();
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
}
- String file = null, protocol = null, format = null, data = null;
+ String file = null, data = null;
+ FileFormatI format = null;
+ DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
- Vector getFeatures = null; // vector of das source nicknames to
- // fetch
- // features from
- // loading is done.
+
String groovyscript = null; // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
@@ -372,118 +515,48 @@ public class Jalview
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
- {
- String viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == jalview.io.FormatAdapter.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == 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://"))
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
- if (!(new File(file)).exists())
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
- 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);
+ }
}
}
}
protocol = AppletFormatAdapter.checkProtocol(file);
- format = new IdentifyFile().identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
@@ -499,19 +572,13 @@ public class Jalview
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColour(af
- .getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
- if (cs == null)
- {
- UserColourScheme ucs = new 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);
}
@@ -523,8 +590,8 @@ public class Jalview
af.parseFeaturesFile(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)
@@ -532,8 +599,8 @@ public class Jalview
af.parseFeaturesFile(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);
@@ -541,8 +608,8 @@ public class Jalview
{
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"))
@@ -573,18 +640,14 @@ public class Jalview
data = aparser.getValue("tree", true);
if (data != null)
{
- jalview.io.NewickFile fin = null;
try
{
- System.out.println("CMD [-tree " + data
- + "] executed successfully!");
- fin = new NewickFile(data,
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
- if (fin != null)
- {
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- }
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
@@ -594,27 +657,6 @@ public class Jalview
// 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
@@ -628,17 +670,17 @@ public class Jalview
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 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 File(file);
imageName = imageFile.getName();
@@ -646,46 +688,54 @@ public class Jalview
System.out.println("Creating SVG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("html"))
+ else if (outputFormat.equalsIgnoreCase("html"))
{
File imageFile = new File(file);
imageName = imageFile.getName();
- new HtmlSvgOutput(new 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("biojsmsa"))
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
{
- BioJsHTMLOutput.updateBioJS();
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
try
{
- Thread.sleep(1500);
- } catch (InterruptedException e)
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
{
e.printStackTrace();
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
- System.out.println("Creating BioJS MSA Viwer HTML file: "
- + file);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out
+ .println("Creating BioJS MSA Viwer HTML file: " + file);
continue;
}
- else if (format.equalsIgnoreCase("imgMap"))
+ 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 File(file);
- System.out.println("Creating EPS file: "
- + outputFile.getAbsolutePath());
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
af.createEPS(outputFile);
continue;
}
- if (af.saveAlignment(file, format))
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
{
System.out.println("Written alignment in " + format
+ " format to " + file);
@@ -709,54 +759,53 @@ public class Jalview
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ if (!Platform.isJS() && !headless && file == null
+ && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- file = jalview.bin.Cache.getDefault(
- "STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ 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"))
+ if (file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_3.jar"))
{
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
// and remove the stale setting
- jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ Cache.removeProperty("STARTUP_FILE");
}
- protocol = "File";
+ protocol = DataSourceType.FILE;
- if (file.indexOf("http:") > -1)
+ if (HttpUtils.startsWithHttpOrHttps(file))
{
- protocol = "URL";
+ protocol = DataSourceType.URL;
}
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
- format = new 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)
{
@@ -767,8 +816,8 @@ public class Jalview
}
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);
}
}
@@ -783,10 +832,213 @@ public class Jalview
}
}
+ 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.isMac())
+ {
+ setMacLookAndFeel();
+ }
+ }
+ }
+
+ private static boolean setCrossPlatformLookAndFeel()
+ {
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(
+ 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 setSystemLookAndFeel()
+ {
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ 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"
@@ -814,15 +1066,12 @@ public class Jalview
+ "-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");
}
@@ -832,10 +1081,8 @@ public class Jalview
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new 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)",
@@ -844,8 +1091,8 @@ public class Jalview
@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.");
}
@@ -885,10 +1132,10 @@ public class Jalview
try
{
tfile = File.createTempFile("jalview", "groovy");
- PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(tfile)));
- BufferedReader br = new BufferedReader(new InputStreamReader(
- System.in));
+ 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)
{
@@ -901,8 +1148,8 @@ public class Jalview
} 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;
}
@@ -911,8 +1158,8 @@ public class Jalview
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;
@@ -954,7 +1201,7 @@ public class Jalview
}
try
{
- Map vbinding = new HashMap();
+ Map vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
@@ -978,95 +1225,6 @@ public class Jalview
}
}
- /**
- * 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;
- 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 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");