import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
}
}
+ // set individual session preferences
+ if (bootstrapArgs.contains(Arg.P))
+ {
+ for (String kev : bootstrapArgs.getValueList(Arg.P))
+ {
+ if (kev == null)
+ {
+ continue;
+ }
+ int equalsIndex = kev.indexOf(ArgParser.EQUALS);
+ if (equalsIndex > -1)
+ {
+ String key = kev.substring(0, equalsIndex);
+ String val = kev.substring(equalsIndex + 1);
+ Cache.setSessionProperty(key, val);
+ }
+ }
+ }
+
// Move any new getdown-launcher-new.jar into place over old
// getdown-launcher.jar
String appdirString = System.getProperty("getdownappdir");
{
headless = true;
}
- System.setProperty("http.agent",
- "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+ System.setProperty("http.agent", HttpUtils.getUserAgent());
try
{
testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
}
- boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+ boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
if (aparser.contains("nousagestats"))
usagestats = false;
if (usagestats)
{
startUsageStats(desktop);
- testoutput(argparser, Arg.USAGESTATS);
+ testoutput(argparser, Arg.NOUSAGESTATS);
}
else
{
System.out.println("CMD [-nousagestats] executed successfully!");
- testoutput(argparser, Arg.USAGESTATS);
+ testoutput(argparser, Arg.NOUSAGESTATS);
}
boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
// Run Commands from cli
cmds = new Commands(argparser, headlessArg);
boolean commandsSuccess = cmds.argsWereParsed();
+
if (commandsSuccess)
{
if (headlessArg)
ex.printStackTrace(System.err);
}
}
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
+
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
+ try
{
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
+ String outputFormat = aparser.nextValue();
+ file = aparser.nextValue();
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
+ if (outputFormat.equalsIgnoreCase("png"))
{
- System.err.println("The output html file must not be null");
- return;
+ System.out.println("Creating PNG image: " + file);
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ continue;
}
- try
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ System.out.println("Creating SVG image: " + file);
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
{
- e.printStackTrace();
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+
+ System.out.println("Creating HTML image: " + file);
+ htmlSVG.exportHTML(file);
+ continue;
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out
- .println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
- FileFormatI outFormat = null;
- try
- {
- outFormat = FileFormats.getInstance().forName(outputFormat);
- } catch (Exception formatP)
- {
- System.out.println("Couldn't parse " + outFormat
- + " as a valid Jalview format string.");
- }
- if (outFormat != null)
- {
- if (!outFormat.isWritable())
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
{
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
System.out.println(
- "This version of Jalview does not support alignment export as "
- + outputFormat);
+ "Creating BioJS MSA Viwer HTML file: " + file);
+ bjs.exportHTML(file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ System.out.println("Creating image map: " + file);
+ af.createImageMap(new File(file), imageName);
+ continue;
}
- else
+ else if (outputFormat.equalsIgnoreCase("eps"))
{
- af.saveAlignment(file, outFormat);
- if (af.isSaveAlignmentSuccessful())
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
+ }
+ if (outFormat != null)
+ {
+ if (!outFormat.isWritable())
{
- System.out.println("Written alignment in "
- + outFormat.getName() + " format to " + file);
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
}
else
{
- System.out.println("Error writing file " + file + " in "
- + outFormat.getName() + " format!!");
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
+ }
}
}
+ } catch (ImageOutputException ioexc)
+ {
+ System.out.println(
+ "Unexpected error whilst exporting image to " + file);
+ ioexc.printStackTrace();
}
}
if (!Platform.isJS() && !headless && file == null
&& Cache.getDefault("SHOW_STARTUP_FILE", true)
- && !cmds.commandArgsProvided())
+ && !cmds.commandArgsProvided()
+ && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
// don't open the startup file if command line args have been processed
// (&& !Commands.commandArgsProvided())
/**
private static void setLookAndFeel()
{
- // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
- // "mac" or "flat"
- // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
- // try Quaqua/Vaqua.
- String lafProp = System.getProperty("laf");
- String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
- String laf = "none";
- if (lafProp != null)
- {
- laf = lafProp;
- }
- else if (lafSetting != null)
- {
- laf = lafSetting;
- }
- boolean lafSet = false;
- switch (laf)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- case "crossplatform":
- lafSet = setCrossPlatformLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+ // "mac" or "flat"
+ // If not set (or chosen laf fails), use the normal SystemLaF and if on
+ // Mac,
+ // try Quaqua/Vaqua.
+ String lafProp = System.getProperty("laf");
+ String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+ String laf = "none";
+ if (lafProp != null)
+ {
+ laf = lafProp;
}
- break;
- case "system":
- lafSet = setSystemLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
- }
- break;
- case "gtk":
- lafSet = setGtkLookAndFeel();
- if (!lafSet)
+ else if (lafSetting != null)
{
- Console.error("Could not set requested laf=" + laf);
+ laf = lafSetting;
}
- break;
- case "metal":
- lafSet = setMetalLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
- }
- break;
- case "nimbus":
- lafSet = setNimbusLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
- }
- break;
- case "flat":
- lafSet = setFlatLookAndFeel();
- if (!lafSet)
+ boolean lafSet = false;
+ switch (laf)
{
- Console.error("Could not set requested laf=" + laf);
- }
- break;
- case "mac":
- lafSet = setMacLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
+ case "crossplatform":
+ lafSet = setCrossPlatformLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "system":
+ lafSet = setSystemLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "gtk":
+ lafSet = setGtkLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "metal":
+ lafSet = setMetalLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "nimbus":
+ lafSet = setNimbusLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "flat":
+ lafSet = setFlatLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "mac":
+ lafSet = setMacLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "none":
+ break;
+ default:
+ Console.error("Requested laf=" + laf + " not implemented");
}
- break;
- case "none":
- break;
- default:
- Console.error("Requested laf=" + laf + " not implemented");
- }
- if (!lafSet)
- {
- // Flatlaf default for everyone!
- lafSet = setFlatLookAndFeel();
if (!lafSet)
{
- setSystemLookAndFeel();
- }
- if (Platform.isLinux())
- {
- setLinuxLookAndFeel();
- }
- if (Platform.isMac())
- {
- setMacLookAndFeel();
+ // Flatlaf default for everyone!
+ lafSet = setFlatLookAndFeel();
+ if (!lafSet)
+ {
+ setSystemLookAndFeel();
+ }
+ if (Platform.isLinux())
+ {
+ setLinuxLookAndFeel();
+ }
+ if (Platform.isMac())
+ {
+ setMacLookAndFeel();
+ }
}
}
}
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ "-nonews\tTurn off check for Jalview news.\n"
- + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ + "-nousagestats\tTurn off 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,
* start a User Config prompt asking if we can log 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)",
+ "USAGESTATS",
+ MessageManager.getString("prompt.plausible_analytics_title"),
+ MessageManager.getString("prompt.plausible_analytics"),
new Runnable()
{
@Override
public void run()
{
- Console.debug(
- "Initialising googletracker for usage stats.");
- Cache.initGoogleTracker();
+ Console.debug("Initialising analytics for usage stats.");
+ Cache.initAnalytics();
Console.debug("Tracking enabled.");
}
}, new Runnable()
@Override
public void run()
{
- Console.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling analytics.");
}
}, null, true);
desktop.addDialogThread(prompter);
}
}
- /*
- * testoutput for string values
+ /******************************
+ *
+ * TEST OUTPUT METHODS
+ *
+ ******************************/
+ /**
+ * method for reporting string values parsed/processed during tests
+ *
*/
protected static void testoutput(ArgParser ap, Arg a, String s1,
String s2)
testoutput(true, a, s1, s2);
}
+ /**
+ * method for reporting string values parsed/processed during tests
+ */
+
protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
String s2)
{
testoutput(true, a, s1, s2);
}
+ /**
+ * report value set for string values parsed/processed during tests
+ */
private static void testoutput(boolean yes, Arg a, String s1, String s2)
{
if (yes && ((s1 == null && s2 == null)
}
/*
- * testoutput for boolean values
+ * testoutput for boolean and unary values
*/
protected static void testoutput(ArgParser ap, Arg a)
{
private static void testoutput(boolean yes, Arg a)
{
- System.out.println("[TESTOUTPUT] arg "
- + (yes ? a.argString() : a.negateArgString()) + " was set");
+ String message = null;
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ message = (yes ? a.argString() : a.negateArgString()) + " was set";
+ }
+ else if (a.hasOption(Opt.UNARY))
+ {
+ message = a.argString() + (yes ? " was set" : " was not set");
+ }
+ System.out.println("[TESTOUTPUT] arg " + message);
}
}
git://source.jalview.org / jalview.git / blobdiff