*
*/
{
- Console.outputMessage("not in js");
+ Console.outPrintln("not in js");
}
// BH - for event debugging in JavaScript (Java mode only)
if (!quiet() || !bootstrapArgs.outputToStdout()
|| bootstrapArgs.contains(Arg.VERSION))
{
- Console.outputMessage(
+ Console.outPrintln(
"Java version: " + System.getProperty("java.version"));
- Console.outputMessage(
- "Java home: " + System.getProperty("java.home"));
- Console.outputMessage("Java arch: " + System.getProperty("os.arch")
- + " " + System.getProperty("os.name") + " "
+ Console.outPrintln("Java home: " + System.getProperty("java.home"));
+ Console.outPrintln("Java arch: " + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
- Console.outputMessage("Install4j version: " + val);
+ Console.outPrintln("Install4j version: " + val);
}
val = System.getProperty("installer_template_version");
if (val != null)
{
- Console.outputMessage("Install4j template version: " + val);
+ Console.outPrintln("Install4j template version: " + val);
}
val = System.getProperty("launcher_version");
if (val != null)
{
- Console.outputMessage("Launcher version: " + val);
+ Console.outPrintln("Launcher version: " + val);
}
}
Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
{
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-props " + usrPropsFile + "] executed successfully!");
testoutput(bootstrapArgs, Arg.PROPS,
"test/jalview/bin/testProps.jvprops", usrPropsFile);
{
List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
.getList(Arg.HELP);
- Console.outputMessage(Arg.usage(helpArgs.stream()
- .map(e -> e.getKey()).collect(Collectors.toList())));
+ Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+ .collect(Collectors.toList())));
Jalview.exit(null, 0);
}
if (aparser.contains("help") || aparser.contains("h"))
* Now using new usage statement.
showUsage();
*/
- Console.outputMessage(Arg.usage());
+ Console.outPrintln(Arg.usage());
Jalview.exit(null, 0);
}
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
testoutput(bootstrapArgs, Arg.JABAWS,
"http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
} catch (MalformedURLException e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Invalid jabaws parameter: " + jabawsUrl + " ignored");
}
}
}
else
{
- System.err.println("Executing setprop argument: " + setprop);
+ jalview.bin.Console
+ .errPrintln("Executing setprop argument: " + setprop);
if (Platform.isJS())
{
Cache.setProperty(setprop.substring(0, p),
}
else
{
- Console.outputMessage(
- "CMD [-nousagestats] executed successfully!");
+ Console.outPrintln("CMD [-nousagestats] executed successfully!");
testoutput(argparser, Arg.NOUSAGESTATS);
}
// questionnaire
Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
- Console.outputMessage("CMD questionnaire[-" + url
+ Console.outPrintln("CMD questionnaire[-" + url
+ "] executed successfully!");
}
else
}
else
{
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-noquestionnaire] executed successfully!");
testoutput(argparser, Arg.QUESTIONNAIRE);
}
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- Console.outputMessage(
- "CMD [-open " + file + "] executed successfully!");
+ Console.outPrintln("CMD [-open " + file + "] executed successfully!");
if (!Platform.isJS())
/**
format);
if (af == null)
{
- Console.outputMessage("error");
+ Console.outPrintln("error");
}
else
{
if (cs != null)
{
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-colour " + data + "] executed successfully!");
}
af.changeColour(cs);
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
- // Console.outputMessage("Added " + data);
- Console.outputMessage(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
{
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
- // Console.outputMessage("Added " + data);
- Console.outputMessage(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD [-features " + data + "] executed successfully!");
}
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- // Console.outputMessage("Added " + data);
- Console.outputMessage(
+ // Console.outPrintln("Added " + data);
+ Console.outPrintln(
"CMD [-annotations " + data + "] executed successfully!");
}
// set or clear the sortbytree flag.
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
{
- Console.outputMessage(
- "CMD [-sortbytree] executed successfully!");
+ Console.outPrintln("CMD [-sortbytree] executed successfully!");
}
}
if (aparser.contains("no-annotation"))
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
- Console.outputMessage(
- "CMD no-annotation executed successfully!");
+ Console.outPrintln("CMD no-annotation executed successfully!");
}
}
if (aparser.contains("nosortbytree"))
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-nosortbytree] executed successfully!");
}
}
{
try
{
- Console.outputMessage(
+ Console.outPrintln(
"CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
.setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
- System.err.println("Couldn't add tree " + data);
+ jalview.bin.Console.errPrintln("Couldn't add tree " + data);
ex.printStackTrace(System.err);
}
}
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
- Console.outputMessage("Executing script " + groovyscript);
+ Console.outPrintln("Executing script " + groovyscript);
executeGroovyScript(groovyscript, af);
- Console.outputMessage("CMD groovy[" + groovyscript
+ Console.outPrintln("CMD groovy[" + groovyscript
+ "] executed successfully!");
groovyscript = null;
}
if (outputFormat.equalsIgnoreCase("png"))
{
- Console.outputMessage("Creating PNG image: " + file);
+ Console.outPrintln("Creating PNG image: " + file);
af.createPNG(new File(file));
imageName = (new File(file)).getName();
continue;
}
else if (outputFormat.equalsIgnoreCase("svg"))
{
- Console.outputMessage("Creating SVG image: " + file);
+ Console.outPrintln("Creating SVG image: " + file);
File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- Console.outputMessage("Creating HTML image: " + file);
+ Console.outPrintln("Creating HTML image: " + file);
htmlSVG.exportHTML(file);
continue;
}
{
if (file == null)
{
- System.err.println("The output html file must not be null");
+ jalview.bin.Console.errPrintln(
+ "The output html file must not be null");
return;
}
try
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- Console.outputMessage(
+ Console.outPrintln(
"Creating BioJS MSA Viwer HTML file: " + file);
bjs.exportHTML(file);
continue;
}
else if (outputFormat.equalsIgnoreCase("imgMap"))
{
- Console.outputMessage("Creating image map: " + file);
+ Console.outPrintln("Creating image map: " + file);
af.createImageMap(new File(file), imageName);
continue;
}
else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
- Console.outputMessage(
+ Console.outPrintln(
"Creating EPS file: " + outputFile.getAbsolutePath());
af.createEPS(outputFile);
continue;
outFormat = FileFormats.getInstance().forName(outputFormat);
} catch (Exception formatP)
{
- Console.outputMessage("Couldn't parse " + outFormat
+ Console.outPrintln("Couldn't parse " + outFormat
+ " as a valid Jalview format string.");
}
if (outFormat != null)
{
if (!outFormat.isWritable())
{
- Console.outputMessage(
+ Console.outPrintln(
"This version of Jalview does not support alignment export as "
+ outputFormat);
}
af.saveAlignment(file, outFormat);
if (af.isSaveAlignmentSuccessful())
{
- Console.outputMessage("Written alignment in "
+ Console.outPrintln("Written alignment in "
+ outFormat.getName() + " format to " + file);
}
else
{
- Console.outputMessage("Error writing file " + file
- + " in " + outFormat.getName() + " format!!");
+ Console.outPrintln("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
}
}
}
} catch (ImageOutputException ioexc)
{
- Console.outputMessage(
+ Console.outPrintln(
"Unexpected error whilst exporting image to " + file);
ioexc.printStackTrace();
}
while (aparser.getSize() > 0)
{
- Console.outputMessage("Unknown arg: " + aparser.nextValue());
+ Console.outPrintln("Unknown arg: " + aparser.nextValue());
}
}
}
{
if (Cache.groovyJarsPresent())
{
- Console.outputMessage("Executing script " + groovyscript);
+ Console.outPrintln("Executing script " + groovyscript);
executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ groovyscript);
}
/*
private static void showUsage()
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"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"
} catch (Exception ex)
{
- System.err.println("Failed to read from STDIN into tempfile "
- + ((tfile == null) ? "(tempfile wasn't created)"
- : tfile.toString()));
+ jalview.bin.Console
+ .errPrintln("Failed to read from STDIN into tempfile "
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
ex.printStackTrace();
return;
}
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ tfile.toURI());
x.printStackTrace();
tfile = new File(groovyscript);
if (!tfile.exists())
{
- System.err.println("File '" + groovyscript + "' does not exist.");
+ jalview.bin.Console.errPrintln(
+ "File '" + groovyscript + "' does not exist.");
return;
}
if (!tfile.canRead())
{
- System.err.println("File '" + groovyscript + "' cannot be read.");
+ jalview.bin.Console.errPrintln(
+ "File '" + groovyscript + "' cannot be read.");
return;
}
if (tfile.length() < 1)
{
- System.err.println("File '" + groovyscript + "' is empty.");
+ jalview.bin.Console
+ .errPrintln("File '" + groovyscript + "' is empty.");
return;
}
try
sfile = tfile.getAbsoluteFile().toURI().toURL();
} catch (Exception ex)
{
- System.err.println("Failed to create a file URL for "
+ jalview.bin.Console.errPrintln("Failed to create a file URL for "
+ tfile.getAbsoluteFile());
return;
}
}
} catch (Exception e)
{
- System.err.println("Exception Whilst trying to execute file " + sfile
- + " as a groovy script.");
+ jalview.bin.Console
+ .errPrintln("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
e.printStackTrace(System.err);
}
{
if (exitcode == 0)
{
- Console.outputMessage(message);
+ Console.outPrintln(message);
}
else
{
- System.err.println(message);
+ jalview.bin.Console.errPrintln(message);
}
}
}
if (yes && ((s1 == null && s2 == null)
|| (s1 != null && s1.equals(s2))))
{
- Console.outputMessage("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ "' was set");
}
}
{
message = a.argString() + (yes ? " was set" : " was not set");
}
- Console.outputMessage("[TESTOUTPUT] arg " + message);
+ Console.outPrintln("[TESTOUTPUT] arg " + message);
}
}
git://source.jalview.org / jalview.git / blobdiff