import java.util.Vector;
import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
/**
* Main class for Jalview Application <br>
// 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()
{
}
System.setProperty("java.awt.headless", "true");
headless = true;
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
// anything else!
final String jabawsUrl = aparser.getValue("jabaws");
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
} catch (MalformedURLException e)
{
System.err.println("Invalid jabaws parameter: " + jabawsUrl
} catch (Exception ex)
{
}
- if (new Platform().isAMac())
+ if (Platform.isAMac())
{
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
{
UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
.getLookAndFeel());
- } catch (UnsupportedLookAndFeelException e)
+ } catch (Throwable e)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ System.err.println("Failed to set QuaQua look and feel: "
+ + e.toString());
}
}
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
}
}
}
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
desktop.checkForNews();
}
- BioJsHTMLOutput.updateBioJS();
+ if (!isHeadlessMode())
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
{
if (!headless)
{
- desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("Opening file: " + file);
+ System.out.println("CMD [-open " + file + "] executed successfully!");
if (!file.startsWith("http://"))
{
protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new jalview.io.IdentifyFile().identify(file, protocol);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
ucs.parseAppletParameter(data);
cs = ucs;
}
-
- System.out.println("colour is " + data);
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
af.changeColour(cs);
}
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("CMD [-sortbytree] executed successfully!");
+ }
}
if (aparser.contains("no-annotation"))
{
af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
}
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
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("Added tree " + data);
}
} catch (IOException ex)
{
{
// 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 });
- }
- 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, new Object[] { desktop, af });
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
groovyscript = null;
}
String imageName = "unnamed.png";
}
else if (format.equalsIgnoreCase("eps"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
+ File outputFile = new java.io.File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
continue;
}
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new jalview.io.IdentifyFile().identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, new Object[] { desktop,
+ startUpAlframe });
}
else
{
+ "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ "\n\n(you can enable or disable usage tracking in the preferences)",
new Runnable()
{
+ @Override
public void run()
{
Cache.log
}
}, new Runnable()
{
+ @Override
public void run()
{
Cache.log.debug("Not enabling Google Tracking.");
Object[] binding;
int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
+ String cnames[] = new String[] { "Jalview", "currentAlFrame" };
bspec = new Class[blen * 2];
binding = new Object[blen * 2];
blen = 0;
}
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 });
+ 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)
{
}
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)
{
}
return ff;
}
+
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
}
/**
class rnabuttonlistener implements ActionListener
{
+ @Override
public void actionPerformed(ActionEvent arg0)
{
System.out.println("Good idea ! ");
class pbuttonlistener implements ActionListener
{
+ @Override
public void actionPerformed(ActionEvent arg0)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
synchronized (us)
running++;
}
- af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
return queued == 0 && running == 0;
}
-};
+}
git://source.jalview.org / jalview.git / blobdiff