- System.out.println("Java home: " + System.getProperty("java.home"));
- System.out.println("Java arch: " + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
+ Console.outputMessage(
+ "Java home: " + System.getProperty("java.home"));
+ Console.outputMessage("Java arch: " + System.getProperty("os.arch")
+ + " " + System.getProperty("os.name") + " "
"CMD [-props " + usrPropsFile + "] executed successfully!");
testoutput(bootstrapArgs, Arg.PROPS,
"test/jalview/bin/testProps.jvprops", usrPropsFile);
"CMD [-props " + usrPropsFile + "] executed successfully!");
testoutput(bootstrapArgs, Arg.PROPS,
"test/jalview/bin/testProps.jvprops", usrPropsFile);
- System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
- .collect(Collectors.toList())));
+ Console.outputMessage(Arg.usage(helpArgs.stream()
+ .map(e -> e.getKey()).collect(Collectors.toList())));
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
testoutput(bootstrapArgs, Arg.JABAWS,
"http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
testoutput(bootstrapArgs, Arg.JABAWS,
"http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
"CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
"CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
"CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
"CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
af.createPNG(new File(file));
imageName = (new File(file)).getName();
continue;
}
else if (outputFormat.equalsIgnoreCase("svg"))
{
af.createPNG(new File(file));
imageName = (new File(file)).getName();
continue;
}
else if (outputFormat.equalsIgnoreCase("svg"))
{
af.createImageMap(new File(file), imageName);
continue;
}
else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
af.createImageMap(new File(file), imageName);
continue;
}
else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
af.saveAlignment(file, outFormat);
if (af.isSaveAlignmentSuccessful())
{
af.saveAlignment(file, outFormat);
if (af.isSaveAlignmentSuccessful())
{