import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
- 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 -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
System.setProperty("apple.laf.useScreenMenuBar", "true");
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
System.setProperty("apple.laf.useScreenMenuBar", "true");
- 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());
+ }
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
e.printStackTrace();
}
if (vamsasImport != null)
{
// the Jalview specific remnants can now be imported into the new
// session at the user's leisure.
e.printStackTrace();
}
if (vamsasImport != null)
{
// the Jalview specific remnants can now be imported into the new
// session at the user's leisure.
- 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!");
progress = System.currentTimeMillis());
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
- .getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty
+ .getColourScheme(af.getViewport().getAlignment(), data);
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
{
af.loadJalviewDataFile(data, null, null, null);
// System.out.println("Added " + data);
{
af.loadJalviewDataFile(data, null, null, null);
// System.out.println("Added " + data);
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
jalview.bin.Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
jalview.bin.Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
{
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
{
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
+ "-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"
+ "-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"
// +
+ "-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"
// +
+ "-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"
// +
// + "-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");
// + "-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");
- 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)",
"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)",
- 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));
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{