*/
package jalview.bin;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.HtmlSvgOutput;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedReader;
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.io.HtmlSvgOutput;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
/**
* Main class for Jalview Application <br>
* <br>
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
- // if (new 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());
- // System.out
- // .println("--------------------------------------------> in here");
- // } catch (UnsupportedLookAndFeelException e)
- // {
- // // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
- // }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
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
{
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();
}
+ 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.
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://"))
{
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)
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
{ desktop, af });
+
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
}
else
{
}
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;
}
+ "-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"
}
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;
+ }
}
/**
return queued == 0 && running == 0;
}
-};
+}
git://source.jalview.org / jalview.git / blobdiff