*/
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 java.util.Map;
import java.util.Vector;
+import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
/**
* 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 $Revision$
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)
{
void doMain(String[] args)
{
System.setSecurityManager(null);
- System.out.println("Java version: "
- + System.getProperty("java.version"));
+ System.out
+ .println("Java version: " + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
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");
}
}
} 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);
}
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception ex)
{
+ 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");
- try
+ if (lookAndFeel != null)
{
- UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel());
- } 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 set QuaQua 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());
+ }
}
}
// 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
{
// "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);
+ Cache.log.debug(
+ "Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
}
{
if (desktop == null || headless)
{
- System.out
- .println("Headless vamsas sessions not yet supported. Sorry.");
+ 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.
{
if (desktop.joinVamsasSession(vamsasSession))
{
- System.out.println("Successfully joined vamsas session "
- + vamsasSession);
+ System.out.println(
+ "Successfully joined vamsas session " + vamsasSession);
}
else
{
}
} catch (Exception e)
{
- System.err.println("ERROR: Failed to join vamsas session "
- + vamsasSession);
+ 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:
+ Cache.log.info(
+ "Skipping Push for import of data into existing vamsas session."); // TODO:
// enable
// this
// when
{
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!");
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
- .getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty
+ .getColourScheme(af.getViewport().getAlignment(), data);
if (cs != null)
{
- System.out.println("CMD [-color " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
}
af.changeColour(cs);
}
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)
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);
{
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"))
{
try
{
- System.out.println("CMD [-tree " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
- af.getViewport().setCurrentTree(
- af.showNewickTree(nf, data).getTree());
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
}
try
{
- BioJsHTMLOutput
- .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ 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);
+ System.out
+ .println("Creating BioJS MSA Viwer HTML file: " + file);
continue;
}
else if (outputFormat.equalsIgnoreCase("imgMap"))
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 (!headless && file == null && vamsasImport == 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"))
+ 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");
}
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 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"
+ "-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"
+ // "-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,
- "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)",
@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.");
}
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)
{
} 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;
}
try
{
- Map<String, Object> vbinding = new HashMap<String, Object>();
+ Map<String, Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
- if (url != null
- && (url.startsWith("http:") || url
- .startsWith("sequence:http:")))
+ if (url != null && (url.startsWith("http:")
+ || url.startsWith("sequence:http:")))
{
if (nickname == null)
{
locsources += "\t";
}
locsources = locsources + nickname + "|" + url;
- System.err
- .println("NOTE! dasserver parameter not yet really supported (got args of "
+ System.err.println(
+ "NOTE! dasserver parameter not yet really supported (got args of "
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(nickname);
}
- System.out.println("CMD [-dasserver " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-dasserver " + data + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(data);
}
git://source.jalview.org / jalview.git / blobdiff