action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
label.all_known_alignment_files = All known alignment files
+label.command_line_arguments = Command Line Arguments
+warning.using_old_command_line_arguments = It looks like you are using old command line arguments. These are now deprecated and will be removed in a future release of Jalview.\nFind out about the new command line arguments at\n
+warning.using_mixed_command_line_arguments = Jalview cannot use both old (-arg) and new (--arg) command line arguments. Please check your command line arguments.\ne.g. {0} and {1}
+warning.the_following_errors = The following errors and warnings occurred whilst processing files:
prompt.analytics_title = Jalview Estadísticas de Uso
prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
label.all_known_alignment_files = Todos los archivos de alineación conocidos
+label.command_line_arguments = Argumentos de línea de comando
+warning.using_old_command_line_arguments = Parece que estás utilizando argumentos antiguos de línea de comando. Estos ahora están en desuso y se eliminarán en una versión futura de Jalview.\nObtenga más información sobre los nuevos argumentos de la línea de comando en\n
+warning.using_mixed_command_line_arguments = Jalview no puede utilizar argumentos de línea de comando antiguos (-arg) y nuevos (--arg). Verifique los argumentos de su línea de comando.\ne.g. {0} y {1}
+warning.the_following_errors = Se produjeron los siguientes errores y advertencias al procesar archivos:
* <li>WRAP_ALIGNMENT</li>
* <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
* style check</li>
- * <li>BITMAP_SCALE - scale factor for PNG export - default 0 - native resolution</li>
+ * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
+ * resolution</li>
* <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
* <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</li>
* <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Failed to resolve resource " + resourcePath
- + ": " + ex.getMessage());
+ jalview.bin.Console.errPrintln("Failed to resolve resource "
+ + resourcePath + ": " + ex.getMessage());
}
}
else
return def;
}
+ public static float getDefault(String property, float def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Float.parseFloat(string);
+ } catch (NumberFormatException e)
+ {
+ if (!Jalview.quiet())
+ jalview.bin.Console.outPrintln("Error parsing float property '"
+ + property + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
/**
* Answers the value of the given property, or the supplied default value if
* the property is not set
return date_format.parse(val);
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Invalid or corrupt date in property '"
- + propertyName + "' : value was '" + val + "'");
+ jalview.bin.Console
+ .errPrintln("Invalid or corrupt date in property '"
+ + propertyName + "' : value was '" + val + "'");
}
}
return null;
return Integer.valueOf(val);
} catch (NumberFormatException x)
{
- jalview.bin.Console.errPrintln("Invalid integer in property '" + property
- + "' (value was '" + val + "')");
+ jalview.bin.Console.errPrintln("Invalid integer in property '"
+ + property + "' (value was '" + val + "')");
}
}
return null;
private static final Collection<String> bootstrapProperties = new ArrayList<>(
Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
-
public static Properties bootstrapProperties(String filename)
{
Properties bootstrapProps = new Properties();
return null;
if (!file.exists())
{
- jalview.bin.Console.errPrintln("Could not load bootstrap preferences file '"
- + filename + "'");
+ jalview.bin.Console
+ .errPrintln("Could not load bootstrap preferences file '"
+ + filename + "'");
return null;
}
}
} catch (FileNotFoundException e)
{
- jalview.bin.Console.errPrintln("Could not find bootstrap preferences file '"
- + file.getAbsolutePath() + "'");
+ jalview.bin.Console
+ .errPrintln("Could not find bootstrap preferences file '"
+ + file.getAbsolutePath() + "'");
} catch (IOException e)
{
jalview.bin.Console.errPrintln(
import jalview.analysis.AlignmentUtils;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgParser.Position;
private boolean argsWereParsed = false;
+ private List<String> errors = new ArrayList<>();
+
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
}
}
+
+ // report errors
+ Console.warn(
+ "The following errors and warnings occurred whilst processing files:\n"
+ + errorsToString());
+ // gui errors reported in Jalview
+
if (argParser.getBoolean(Arg.QUIT))
{
- Jalview.getInstance().quit();
+ Jalview.getInstance().exit(
+ "Exiting due to " + Arg.QUIT.argString() + " argument.",
+ ExitCode.OK);
return true;
}
// carry on with jalview.bin.Jalview
boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
+ {
return true;
+ }
+
+ Boolean isError = Boolean.valueOf(false);
// set wrap scope here so it can be applied after structures are opened
boolean wrap = false;
{
if (!(new File(openFile)).exists())
{
- Console.warn("Can't find file '" + openFile + "'");
+ addError("Can't find file '" + openFile + "'");
+ isError = true;
continue;
}
}
format = new IdentifyFile().identify(openFile, protocol);
} catch (FileFormatException e1)
{
- Console.error("Unknown file format for '" + openFile + "'");
+ addError("Unknown file format for '" + openFile + "'");
+ isError = true;
continue;
}
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- boolean xception=false;
- try {
+ boolean xception = false;
+ try
+ {
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
} catch (Throwable thr)
{
- xception=true;
- Console.error("Couldn't open '"+openFile+"' as "+format+" "+thr.getLocalizedMessage()+ " (Enable debug for full stack trace)");
- Console.debug("Exception when opening '"+openFile+"'",thr);
- }
- finally
+ xception = true;
+ addError("Couldn't open '" + openFile + "' as " + format + " "
+ + thr.getLocalizedMessage()
+ + " (Enable debug for full stack trace)");
+ isError = true;
+ Console.debug("Exception when opening '" + openFile + "'", thr);
+ } finally
{
- if (af==null && !xception)
+ if (af == null && !xception)
{
- Console.info("Ignoring '"+openFile+"' - no alignment data found.");
+ addInfo("Ignoring '" + openFile
+ + "' - no alignment data found.");
continue;
}
}
if (cs == null && !"None".equals(colour))
{
- Console.warn(
- "Couldn't parse '" + colour + "' as a colourscheme.");
+ addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
}
else
{
"examples/testdata/uniref50_test_tree", treefile);
} catch (IOException e)
{
- Console.warn("Couldn't add tree " + treefile, e);
+ addError("Couldn't add tree " + treefile, e);
+ isError = true;
}
}
{
if (headless)
{
- Jalview.exit("Could not open any files in headless mode", 1);
+ Jalview.exit("Could not open any files in headless mode",
+ ExitCode.NO_FILES);
}
else
{
- Console.warn("No more files to open");
+ Console.info("No more files to open");
}
}
if (progressBarSet && desktop != null)
if (seq == null)
{
- Console.warn("Could not find sequence for argument "
+ addWarn("Could not find sequence for argument "
+ Arg.STRUCTURE.argString() + "=" + val);
- // you probably want to continue here, not break
- // break;
continue;
}
File structureFile = null;
if (structureFile == null)
{
- Console.warn("Not provided structure file with '" + val + "'");
+ addWarn("Not provided structure file with '" + val + "'");
continue;
}
if (!structureFile.exists())
{
- Console.warn("Structure file '"
- + structureFile.getAbsoluteFile() + "' not found.");
+ addWarn("Structure file '" + structureFile.getAbsoluteFile()
+ + "' not found.");
continue;
}
} catch (IOException e)
{
paeFilepath = paeFile.getAbsolutePath();
- Console.warn("Problem with the PAE file path: '"
+ addWarn("Problem with the PAE file path: '"
+ paeFile.getPath() + "'");
}
}
if (it.hasNext())
sb.append(", ");
}
- Console.warn(sb.toString());
+ addWarn(sb.toString());
}
}
if (sv == null)
{
- Console.error("Failed to import and open structure view.");
+ addError("Failed to import and open structure view for file '"
+ + structureFile + "'.");
continue;
}
try
}
if (tries == 0 && sv.isBusy())
{
- Console.warn(
- "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ addWarn("Gave up waiting for structure viewer to load file '"
+ + structureFile
+ + "'. Something may have gone wrong.");
}
} catch (Exception x)
{
- Console.warn("Exception whilst waiting for structure viewer "
+ addError("Exception whilst waiting for structure viewer "
+ structureFilepath, x);
+ isError = true;
}
// add StructureViewer to svMap list
typeS.toUpperCase(Locale.ROOT));
} catch (IllegalArgumentException e)
{
- Console.warn("Do not know image format '" + typeS
+ addWarn("Do not know image format '" + typeS
+ "', using PNG");
imageType = TYPE.PNG;
}
AppJmol jmol = (AppJmol) sview;
try
{
+ boolean success = this.checksBeforeWritingToFile(avm,
+ subVals, false, structureImageFilename,
+ "structure image", isError);
+ if (!success)
+ {
+ continue;
+ }
+
Console.debug("Rendering image to " + structureImageFile);
jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
} catch (ImageOutputException ioexc)
{
- Console.warn("Unexpected error whilst exporting image to "
+ addError("Unexpected error whilst exporting image to "
+ structureImageFile, ioexc);
+ isError = true;
+ continue;
}
}
break;
default:
- Console.warn("Cannot export image for structure viewer "
+ addWarn("Cannot export image for structure viewer "
+ sv.getViewerType() + " yet");
- break;
+ continue;
}
}
}
}
*/
- return theseArgsWereParsed;
+ return theseArgsWereParsed && !isError;
}
protected void processGroovyScript(String id)
if (af == null)
{
- Console.warn("Did not have an alignment window for id=" + id);
+ addWarn("Did not have an alignment window for id=" + id);
return;
}
if (af == null)
{
- Console.warn("Did not have an alignment window for id=" + id);
+ addWarn("Did not have an alignment window for id=" + id);
return false;
}
+ Boolean isError = Boolean.valueOf(false);
if (avm.containsArg(Arg.IMAGE))
{
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
+
+ boolean success = checksBeforeWritingToFile(avm, subVal, false,
+ fileName, "image", isError);
+ if (!success)
+ {
+ continue;
+ }
+
try
{
switch (type)
break;
default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
+ addWarn(Arg.IMAGE.argString() + " type '" + type
+ "' not known. Ignoring");
break;
}
} catch (Exception ioex)
{
- Console.warn("Unexpected error during export", ioex);
+ addError("Unexpected error during export to '" + fileName + "'",
+ ioex);
+ isError = true;
}
}
}
- return true;
+ return !isError;
}
protected boolean processOutput(String id)
if (af == null)
{
- Console.warn("Did not have an alignment window for id=" + id);
+ addWarn("Did not have an alignment window for id=" + id);
return false;
}
+ Boolean isError = Boolean.valueOf(false);
+
if (avm.containsArg(Arg.OUTPUT))
{
for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
String fileName = subVals.getContent();
boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
- boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
- Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
- // backups. Use the Arg.BACKUPS or subval "backups" setting first,
- // otherwise if headless assume false, if not headless use the user
- // preference with default true.
- boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
- subVals, null,
- Platform.isHeadless() ? null : BackupFiles.ENABLED,
- !Platform.isHeadless());
-
- // if backups is not true then --overwrite must be specified
- if (file.exists() && !(overwrite || backups || stdout))
- {
- Console.error("Won't overwrite file '" + fileName + "' without "
- + Arg.OVERWRITE.argString() + " or "
- + Arg.BACKUPS.argString() + " set");
- return false;
- }
String name = af.getName();
String format = ArgParser.getValueFromSubValOrArg(avm, av,
validSB.append(")");
}
- Jalview.exit("No valid format specified for "
+ addError("No valid format specified for "
+ Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", 1);
- // this return really shouldn't happen
- return false;
+ + validSB.toString() + ".");
+ continue;
}
}
- String savedBackupsPreference = Cache
- .getDefault(BackupFiles.ENABLED, null);
- Console.debug("Setting backups to " + backups);
- Cache.applicationProperties.put(BackupFiles.ENABLED,
- Boolean.toString(backups));
+ boolean success = checksBeforeWritingToFile(avm, subVals, true,
+ fileName, ff.getName(), isError);
+ if (!success)
+ {
+ continue;
+ }
+
+ boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+ subVals, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
Console.info("Writing " + fileName);
- af.saveAlignment(fileName, ff, stdout);
- Console.debug("Returning backups to " + savedBackupsPreference);
- if (savedBackupsPreference != null)
- Cache.applicationProperties.put(BackupFiles.ENABLED,
- savedBackupsPreference);
+ af.saveAlignment(fileName, ff, stdout, backups);
if (af.isSaveAlignmentSuccessful())
{
Console.debug("Written alignment '" + name + "' in "
- + ff.getName() + " format to " + file);
+ + ff.getName() + " format to '" + file + "'");
}
else
{
- Console.warn("Error writing file " + file + " in " + ff.getName()
+ addError("Error writing file '" + file + "' in " + ff.getName()
+ " format!");
+ isError = true;
+ continue;
}
}
}
- return true;
+ return !isError;
}
private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
}
return svs;
}
+
+ private void addInfo(String errorMessage)
+ {
+ Console.info(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addWarn(String errorMessage)
+ {
+ Console.warn(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addError(String errorMessage)
+ {
+ addError(errorMessage, null);
+ }
+
+ private void addError(String errorMessage, Exception e)
+ {
+ Console.error(errorMessage, e);
+ errors.add(errorMessage);
+ }
+
+ private boolean checksBeforeWritingToFile(ArgValuesMap avm,
+ SubVals subVal, boolean includeBackups, String filename,
+ String adjective, Boolean isError)
+ {
+ File file = new File(filename);
+
+ boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE,
+ subVal, null, "OVERWRITE_OUTPUT", false);
+ boolean stdout = false;
+ boolean backups = false;
+ if (includeBackups)
+ {
+ stdout = ArgParser.STDOUTFILENAME.equals(filename);
+ // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+ // otherwise if headless assume false, if not headless use the user
+ // preference with default true.
+ backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal,
+ null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+ }
+
+ if (file.exists() && !(overwrite || backups || stdout))
+ {
+ addWarn("Won't overwrite file '" + filename + "' without "
+ + Arg.OVERWRITE.argString()
+ + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+ + " set");
+ return false;
+ }
+
+ boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS,
+ subVal, null, "MKDIRS_OUTPUT", false);
+
+ if (!FileUtils.checkParentDir(file, mkdirs))
+ {
+ addError("Directory '"
+ + FileUtils.getParentDir(file).getAbsolutePath()
+ + "' does not exist for " + adjective + " file '" + filename
+ + "'."
+ + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
+ isError = true;
+ return false;
+ }
+
+ return true;
+ }
+
+ public List<String> getErrors()
+ {
+ return errors;
+ }
+
+ public String errorsToString()
+ {
+ StringBuilder sb = new StringBuilder();
+ for (String error : errors)
+ {
+ if (sb.length() > 0)
+ sb.append("\n");
+ sb.append("- " + error);
+ }
+ return sb.toString();
+ }
}
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.PromptUserConfig;
import jalview.gui.QuitHandler;
import jalview.gui.QuitHandler.QResponse;
// stop now if only after --version
if (bootstrapArgs.contains(Arg.VERSION))
{
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
// old ArgsParser
error.printStackTrace();
String message = "\nEssential logging libraries not found."
+ "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
- Jalview.exit(message, 0);
+ Jalview.exit(message, ExitCode.OK);
}
// register SIGTERM listener
.getList(Arg.HELP);
Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
.collect(Collectors.toList())));
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
*/
Console.outPrintln(Arg.usage());
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
// new CLI
error.printStackTrace();
String message = "\nEssential logging libraries not found."
+ "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
- Jalview.exit(message, 0);
+ Jalview.exit(message, ExitCode.OK);
}
desktop = null;
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
+ mixedCliWarning();
+
try
{
JalviewTaskbar.setTaskbar(this);
}
}
}
+ else
+ {
+
+ if (getArgParser().isMixedStyle())
+ {
+ String warning = MessageManager.formatMessage(
+ "warning.using_mixed_command_line_arguments",
+ getArgParser().getMixedExamples());
+ Console.warn(warning);
+ Jalview.exit(
+ "Exiting due to mixed old and new command line arguments",
+ ExitCode.INVALID_ARGUMENT);
+ }
+ if (getArgParser().isOldStyle())
+ {
+ String warning = MessageManager
+ .getString("warning.using_old_command_line_arguments")
+ .replace("\n", " ")
+ + "https://www.jalview.org/help/html/features/commandline.html";
+ Console.warn(warning);
+ }
+
+ }
+
// Run Commands from cli
cmds = new Commands(argparser, headlessArg);
cmds.processArgs();
else
{
Jalview.exit("Successfully completed commands in headless mode",
- 0);
+ ExitCode.OK);
}
}
Console.info("Successfully completed commands");
{
if (headlessArg)
{
- Jalview.exit("Error when running Commands in headless mode", 1);
+ Jalview.exit("Error when running Commands in headless mode",
+ ExitCode.ERROR_RUNNING_COMMANDS);
}
Console.warn("Error when running commands");
}
if (file == null && desktop == null && !commandsSuccess)
{
- Jalview.exit("No files to open!", 1);
+ Jalview.exit("No files to open!", ExitCode.NO_FILES);
}
long progress = -1;
if (headless)
{
Jalview.exit(
- "Can't find file '" + file + "' in headless mode", 1);
+ "Can't find file '" + file + "' in headless mode",
+ ExitCode.FILE_NOT_FOUND);
}
Console.warn("Can't find file'" + file + "'");
}
}
desktop.setInBatchMode(false);
}
+
+ cliWarning();
}
private static void setLookAndFeel()
public void quit()
{
// System.exit will run the shutdownHook first
- Jalview.exit("Quitting now. Bye!", 0);
+ Jalview.exit("Quitting now. Bye!", ExitCode.OK);
}
public static AlignFrame getCurrentAlignFrame()
return cmds;
}
- public static void exit(String message, int exitcode)
+ public static void exit(String message, ExitCode ec)
{
+ int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
if (Console.log == null)
{
// Don't start the logger just to exit!
}
}
+ public enum ExitCode
+ {
+ // only add new ones to the end of the list (to preserve ordinal values)
+ OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
+ INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
+ ERROR_RUNNING_COMMANDS;
+ }
+
/******************************
*
* TEST OUTPUT METHODS
* @param a
* - Arg currently being processed
* @param s1
- * - expected
+ * - expected
* @param s2
*/
protected static void testoutput(ArgParser ap, Arg a, String s1,
}
/**
- * conditionally (on @param yes) report that expected value s1 was set during CommandsTest tests
+ * conditionally (on @param yes) report that expected value s1 was set during
+ * CommandsTest tests
*/
private static void testoutput(boolean yes, Arg a, String s1, String s2)
{
public static boolean isBatchMode()
{
- return getInstance()!=null && (getInstance().desktop == null || getInstance().desktop.isInBatchMode());
+ return getInstance() != null && (getInstance().desktop == null
+ || getInstance().desktop.isInBatchMode());
+ }
+
+ /**
+ * Warning about old or mixed command line arguments
+ */
+ private void mixedCliWarning()
+ {
+ Jalview j = Jalview.getInstance();
+ boolean mixedStyle = j.getArgParser() != null
+ && j.getArgParser().isMixedStyle();
+ String title = MessageManager.getString("label.command_line_arguments");
+ if (mixedStyle)
+ {
+ String warning = MessageManager.formatMessage(
+ "warning.using_mixed_command_line_arguments",
+ j.getArgParser().getMixedExamples());
+ String quit = MessageManager.getString("action.quit");
+
+ Desktop.instance.nonBlockingDialog(title, warning, quit,
+ JvOptionPane.WARNING_MESSAGE, false, true);
+
+ Jalview.exit(
+ "Exiting due to mixed old and new command line arguments.",
+ ExitCode.MIXED_CLI_ARGUMENTS);
+ }
+ }
+
+ private void cliWarning()
+ {
+ Jalview j = Jalview.getInstance();
+ Commands c = j.getCommands();
+ boolean oldStyle = j.getArgParser() != null
+ && j.getArgParser().isOldStyle();
+ String title = MessageManager.getString("label.command_line_arguments");
+ if (oldStyle)
+ {
+ String warning = MessageManager
+ .getString("warning.using_old_command_line_arguments");
+ String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
+ if (Desktop.instance != null)
+ {
+ String cont = MessageManager.getString("label.continue");
+
+ Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
+ JvOptionPane.WARNING_MESSAGE, false, true, true);
+ }
+ }
+ if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
+ {
+ if (Desktop.instance != null)
+ {
+ String message = MessageManager
+ .getString("warning.the_following_errors");
+ String ok = MessageManager.getString("action.ok");
+ int shortest = 60;
+ List<String> errors = j.getCommands().getErrors();
+ for (int i = 0; i < errors.size(); i++)
+ {
+ shortest = Math.min(shortest, errors.get(i).length());
+ }
+ Desktop.instance.nonBlockingDialog(
+ Math.max(message.length(), Math.min(60, shortest)),
+ Math.min(errors.size(), 20), title, message,
+ j.getCommands().errorsToString(), ok,
+ JvOptionPane.WARNING_MESSAGE, true, false, true);
+ }
+ }
}
}
// Initialising arguments (BOOTSTRAP)
HELP(Type.HELP, "h", "Display basic help", Opt.UNARY, Opt.BOOTSTRAP,
- Opt.HASTYPE, Opt.MULTI),
+ Opt.HASTYPE, Opt.MULTIVALUE),
/*
* Other --help-type Args will be added by the static block.
*/
Opt.BOOTSTRAP, Opt.SECRET),
QUIET(Type.CONFIG, "q",
"Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.",
- Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.BOOTSTRAP),
INITSUBSTITUTIONS(Type.CONFIG,
"Set ‑‑substitutions to be initially enabled (or initially disabled).",
true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
P(Type.CONFIG, "Set a Jalview preference value for this session.",
Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
- Opt.MULTI, Opt.NOACTION, Opt.SECRET), // keep this secret for now.
+ Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for
+ // now.
// Opening an alignment
OPEN(Type.OPENING,
"Opens one or more alignment files or URLs in new alignment windows.",
- Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTI,
- Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.STORED,
- Opt.PRIMARY),
+ Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
+ Opt.MULTIVALUE, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT,
+ Opt.STORED, Opt.PRIMARY),
APPEND(Type.OPENING,
"Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.PRIMARY),
TITLE(Type.OPENING,
"Specifies the title for the open alignment window as string.",
- Opt.STRING, Opt.LINKED),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
"Applies the colour scheme to the open alignment window. Valid values include:\n"
+ "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
+ "Names of user defined colourschemes will also work,\n"
+ "and jalview colourscheme specifications like\n"
+ "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
TREE(Type.OPENING, "Add a tree file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
SORTBYTREE(Type.OPENING,
"Enforces sorting (or not sorting) the open alignment in the order of an attached phylogenetic tree.",
- true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWALL),
+ true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWMULTIID),
ANNOTATIONS(Type.OPENING,
"Add an annotations file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
SHOWANNOTATIONS(Type.OPENING,
"Enforces showing (or not showing) alignment annotations.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
WRAP(Type.OPENING,
"Enforces wrapped (or not wrapped) alignment formatting.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
NOSTRUCTURE(Type.OPENING,
"Do not open or process any 3D structure in the ‑‑open or ‑‑append files.",
- Opt.UNARY, Opt.LINKED, Opt.ALLOWALL),
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
// Adding a 3D structure
STRUCTURE(Type.STRUCTURE,
"Load a structure file or URL associated with a sequence in the open alignment.\n"
+ "The sequence to be associated with can be specified with a following --seqid argument, or the subval modifier seqid=ID can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS,
- Opt.PRIMARY),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.PRIMARY, Opt.ALLOWMULTIID),
SEQID(Type.STRUCTURE,
"Specify the sequence name for the preceding --structure to be associated with.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
PAEMATRIX(Type.STRUCTURE,
"Add a PAE json matrix file to the preceding --structure.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
TEMPFAC(Type.STRUCTURE,
"Set the type of temperature factor. Possible values are:\n"
+ "default,\n" + "plddt.",
- Opt.STRING, Opt.LINKED),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREVIEWER(Type.STRUCTURE,
"Set the structure viewer to use to open the 3D structure file specified in previous --structure to name. Possible values of name are:\n"
+ "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
+ "pymol.",
- Opt.STRING, Opt.LINKED, Opt.MULTI),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
- Opt.UNARY, Opt.LINKED, Opt.ALLOWALL, Opt.SECRET), // keep this secret
- // until it works!
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
+ // secret
+ // until it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
- Opt.ALLOWALL),
+ Opt.ALLOWMULTIID),
// Outputting files
IMAGE(Type.IMAGE,
"Output an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are:\n"
+ "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWMULTIID,
Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
TYPE(Type.IMAGE,
"Set the image format for the preceding --image. Valid values are:\n"
+ "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
TEXTRENDERER(Type.IMAGE,
"Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+ "text,\n" + "lineart.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
SCALE(Type.IMAGE,
"Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
WIDTH(Type.IMAGE,
"Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
HEIGHT(Type.IMAGE,
"Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
"Export an image of a 3D structure opened in JMOL", Opt.STRING,
- Opt.LINKED, Opt.MULTI, Opt.OUTPUTFILE),
+ Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID),
STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE,
"Set the structure image format for the preceding --structureimage. Valid values are:\n"
+ "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGETEXTRENDERER(Type.STRUCTUREIMAGE,
"Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+ "text,\n" + "lineart.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGESCALE(Type.STRUCTUREIMAGE,
"Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGEWIDTH(Type.STRUCTUREIMAGE,
"Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGEHEIGHT(Type.STRUCTUREIMAGE,
"Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
OUTPUT(Type.OUTPUT,
"Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ "pileup (pileup),\n" + "msf (msf),\n"
+ "clustal (aln),\n" + "phylip (phy),\n"
+ "jalview (jvp, jar).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWMULTIID,
Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
FORMAT(Type.OUTPUT,
"Sets the format for the preceding --output file. Valid formats are:\n"
+ "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
+ "blc,\n" + "amsa,\n" + "json,\n" + "pileup,\n"
+ "msf,\n" + "clustal,\n" + "phylip,\n" + "jalview.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
GROOVY(Type.PROCESS,
"Process a groovy script in the file for the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS,
- Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
BACKUPS(Type.OUTPUT,
"Enable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
- true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID),
OVERWRITE(Type.OUTPUT,
"Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID),
CLOSE(Type.OPENING,
"Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
- Opt.UNARY, Opt.LINKED, Opt.ALLOWALL),
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
+ MKDIRS(Type.OUTPUT,
+ "Automatically create directories when outputting a file to a new directory.",
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
// controlling flow of arguments
NEW(Type.FLOW,
"Move on to a new alignment window. This will ensure --append will start a new alignment window and other linked arguments will apply to the new alignment window.",
- Opt.UNARY, Opt.MULTI, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION,
+ Opt.INCREMENTDEFAULTCOUNTER),
SUBSTITUTIONS(Type.FLOW,
"The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are:\n"
+ "{basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
+ "{n} - the value of the index counter (starting at 0).\n"
+ "{++n} - increase and substitute the value of the index counter,\n"
+ "{} - the value of the current alignment window default index.",
- true, Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ true, Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
ARGFILE(Type.FLOW,
"Open one or more files filename and read, line-by-line, as arguments to Jalview.\n"
+ "Values in an argfile should be given with an equals sign (\"=\") separator with no spaces.\n"
+ "Note that if you use one or more --argfile arguments then all other non-initialising arguments will be ignored.",
- Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
+ Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS),
NPP(Type.FLOW, "n++",
"Increase the index counter used in argument value substitutions.",
- Opt.UNARY, Opt.MULTI, Opt.NOACTION),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION),
ALL(Type.FLOW,
"Apply the following output arguments to all sets of linked arguments.",
- Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
OPENED(Type.FLOW,
"Apply the following output arguments to all of the last --open'ed set of linked arguments.",
- Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
QUIT(Type.FLOW,
"After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
Opt.UNARY),
Opt.UNARY, Opt.SECRET),
ALLSTRUCTURES(Type.FLOW,
"Apply the following 3D structure formatting arguments to all structures within the open alignment.",
- Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
// secret options
TESTOUTPUT(Type.CONFIG,
"Allow specific stdout information. For testing purposes only.",
Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user
SETPROP(Type.CONFIG, "Set an individual Java System property.",
- Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.SECRET), // not in use yet
+ Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use
+ // yet
NIL(Type.FLOW,
"This argument does nothing on its own, but can be used with linkedIds.",
- Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION, Opt.SECRET),
+ Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET),
// private options (inserted during arg processing)
SETARGFILE(Type.FLOW,
"Sets the current value of the argfilename. Inserted before argfilecontents.",
- Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTI, Opt.PRIVATE,
+ Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTIVALUE, Opt.PRIVATE,
Opt.NOACTION),
UNSETARGFILE(Type.FLOW,
"Unsets the current value of the argfilename. Inserted after argfile contents.",
- Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION),
+ Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.PRIVATE, Opt.NOACTION),
// these last two have no purpose in the normal Jalview application but are
// used by jalview.bin.Launcher to set memory settings. They are not used by
* A MULTI Arg can be specified multiple times.
* Multiple values are stored in the ArgValuesMap (along with their positional index) for each linkedId.
*/
- MULTI("can be specified multiple times"),
+ MULTIVALUE("can be specified multiple times"),
/*
* A Linked Arg can be linked to others through a --arg[linkedId] or --arg[linkedId]=value.
* If no linkedId is specified then the current default linkedId will be used.
/*
* An ALLOWALL Arg can use the '*' linkedId to apply to all known linkedIds
*/
- ALLOWALL("can be used with " + ArgParser.DOUBLEDASH + "all"),
+ ALLOWMULTIID("can be used with " + ArgParser.DOUBLEDASH + "all"),
/*
* If an Arg has the INCREMENTDEFAULTCOUNTER option and the default linkedId is used,
* the defaultLinkedIdCounter is incremented *first*.
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg.Opt;
import jalview.bin.argparser.Arg.Type;
import jalview.util.FileUtils;
private boolean allLinkedIds = false;
/**
- * flag to say whether the default linkedId is the current default linked id
- * or OPENED linkedIds
- */
- private boolean openedLinkedIds = false;
-
- /**
* flag to say whether the structure arguments should be applied to all
* structures with this linked id
*/
private BootstrapArgs bootstrapArgs = null;
+ private boolean oldArguments = false;
+
+ private boolean mixedArguments = false;
+
+ /**
+ * saved examples of mixed arguments
+ */
+ private String[] mixedExamples = new String[] { null, null };
+
static
{
argMap = new HashMap<>();
if (arg.startsWith(DOUBLEDASH))
{
dd = true;
- break;
+ if (mixedExamples[1] == null)
+ {
+ mixedExamples[1] = arg;
+ }
}
- else if (arg.startsWith("-") || arg.equals("open"))
+ else if ((arg.startsWith("-") && !arg.equals(STDOUTFILENAME))
+ || arg.equals("open"))
{
d = true;
+ if (mixedExamples[0] == null)
+ {
+ mixedExamples[0] = arg;
+ }
+ }
+ }
+ if (d)
+ {
+ if (dd)
+ {
+ mixedArguments = true;
+ }
+ else
+ {
+ oldArguments = true;
}
}
- if (d && !dd)
+
+ if (oldArguments || mixedArguments)
{
// leave it to the old style -- parse an empty list
parse(new ArrayList<String>(), false, false);
return;
}
+
if (bsa != null)
this.bootstrapArgs = bsa;
else
{
// arg not found
Console.error("Argument '" + arg + "' not recognised. Exiting.");
- Jalview.exit("Invalid argument used." + System.lineSeparator()
- + "Use" + System.lineSeparator() + "jalview "
- + Arg.HELP.argString() + System.lineSeparator()
- + "for a usage statement.", 13);
+ Jalview.exit(
+ "Invalid argument used." + System.lineSeparator() + "Use"
+ + System.lineSeparator() + "jalview "
+ + Arg.HELP.argString() + System.lineSeparator()
+ + "for a usage statement.",
+ ExitCode.INVALID_ARGUMENT);
continue;
}
if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
else if (a == Arg.ALL)
{
allLinkedIds = !negated;
- openedLinkedIds = false;
- }
- else if (a == Arg.OPENED)
- {
- openedLinkedIds = !negated;
- allLinkedIds = false;
}
else if (a == Arg.ALLSTRUCTURES)
{
{
if (linkedId == null)
{
- if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
- && val.startsWith(MATCHALLLINKEDIDS))
+ if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID)
+ && val.contains(MATCHALLLINKEDIDS))
{
- // --output=*.ext is shorthand for --all --output {basename}.ext
+ // --output=*.ext is shorthand for --output {basename}.ext
+ // --output=*/*.ext is shorthand for
+ // --output {dirname}/{basename}.ext
// (or --image=*.ext)
- allLinkedIds = true;
- openedLinkedIds = false;
- linkedId = MATCHALLLINKEDIDS;
- val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
- + val.substring(MATCHALLLINKEDIDS.length());
+ linkedId = allLinkedIds ? MATCHALLLINKEDIDS
+ : MATCHOPENEDLINKEDIDS;
+ val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS,
+ LINKEDIDDIRNAME, LINKEDIDBASENAME);
}
- else if (a.hasOption(Opt.OUTPUTFILE)
- && a.hasOption(Opt.ALLOWALL)
- && val.startsWith(MATCHOPENEDLINKEDIDS))
- {
- // --output=open*.ext is shorthand for --opened --output
- // {basename}.ext
- // (or --image=open*.ext)
- openedLinkedIds = true;
- allLinkedIds = false;
- linkedId = MATCHOPENEDLINKEDIDS;
- val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
- + val.substring(MATCHOPENEDLINKEDIDS.length());
- }
- else if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+ else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID))
{
linkedId = MATCHALLLINKEDIDS;
}
- else if (openedLinkedIds && a.hasOption(Opt.ALLOWALL))
+ else if (a.hasOption(Opt.ALLOWMULTIID)
+ && this.storedLinkedIds != null
+ && this.storedLinkedIds.size() > 0)
{
linkedId = MATCHOPENEDLINKEDIDS;
}
// remove the '*' or 'open*' linkedId that should be empty if it was
// created
if ((MATCHALLLINKEDIDS.equals(linkedId)
+ || MATCHOPENEDLINKEDIDS.equals(linkedId))
&& linkedArgs.containsKey(linkedId))
- || (MATCHOPENEDLINKEDIDS.equals(linkedId)
- && linkedArgs.containsKey(linkedId)))
{
linkedArgs.remove(linkedId);
}
{
String message = Arg.ARGFILE.argString() + EQUALS + "\""
+ argFile.getPath() + "\": File does not exist.";
- Jalview.exit(message, 2);
+ Jalview.exit(message, ExitCode.FILE_NOT_FOUND);
}
try
{
{
String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ "\": File could not be read.";
- Jalview.exit(message, 3);
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
}
}
// Third param "true" uses Opt.PRIVATE args --setargile=argfile and
String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ "\": File could not be read.";
Console.debug(message, e);
- Jalview.exit(message, 3);
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
}
}
return args;
Arg a = avs.arg();
List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
+ if (a.hasOption(Opt.ALLOWMULTIID))
{
switch (linkedId)
{
// skip incorrectly stored wildcard ids!
if (id == null || MATCHALLLINKEDIDS.equals(id)
|| MATCHOPENEDLINKEDIDS.equals(id))
+ {
continue;
+ }
ArgValuesMap avm = linkedArgs.get(id);
// don't set an output if there isn't an input
if (a.hasOption(Opt.REQUIREINPUT)
return linkedArgs.get(linkedId);
}
+ public boolean isOldStyle()
+ {
+ return oldArguments;
+ }
+
+ public boolean isMixedStyle()
+ {
+ return mixedArguments;
+ }
+
+ public String[] getMixedExamples()
+ {
+ return mixedExamples;
+ }
}
\ No newline at end of file
protected void addArgValue(ArgValue av, boolean beingSetByWildcard)
{
// allow a non-wildcard value to overwrite a wildcard set single value
- boolean overwrite = !arg.hasOption(Opt.MULTI) && setByWildcard
+ boolean overwrite = !arg.hasOption(Opt.MULTIVALUE) && setByWildcard
&& !beingSetByWildcard;
- if ((!arg.hasOption(Opt.MULTI) && argValueList.size() > 0)
+ if ((!arg.hasOption(Opt.MULTIVALUE) && argValueList.size() > 0)
&& !overwrite)
return;
if (arg.hasOption(Opt.NODUPLICATEVALUES)
protected ArgValue getArgValue()
{
- if (arg.hasOption(Opt.MULTI))
+ if (arg.hasOption(Opt.MULTIVALUE))
Console.warn("Requesting single value for multi value argument");
return argValueList.size() > 0 ? argValueList.get(0) : null;
}
*/
public String getBasename()
{
- return getDirBasenameOrExtension(false, false);
+ return getDirBasenameOrExtension(false, false, false);
}
/*
*/
public String getExtension()
{
- return getDirBasenameOrExtension(false, true);
+ return getDirBasenameOrExtension(false, true, false);
}
/*
*/
public String getDirname()
{
- return getDirBasenameOrExtension(true, false);
+ return getDirBasenameOrExtension(true, false, false);
}
public String getDirBasenameOrExtension(boolean dirname,
- boolean extension)
+ boolean extension, boolean absoluteDirname)
{
String filename = null;
String appendVal = getValue(Arg.APPEND);
private void add(Arg a, Type t, String s)
{
List<Map.Entry<Type, String>> l = getOrCreateList(a);
- if (a.hasOption(Opt.MULTI) || l.size() == 0)
+ if (a.hasOption(Opt.MULTIVALUE) || l.size() == 0)
{
l.add(entry(t, s));
}
private void addAll(Arg a, Type t, List<String> al)
{
List<Map.Entry<Type, String>> l = getOrCreateList(a);
- if (a.hasOption(Opt.MULTI))
+ if (a.hasOption(Opt.MULTIVALUE))
{
for (String s : al)
{
*/
public void saveAlignment(String file, FileFormatI format)
{
- saveAlignment(file, format, false);
+ saveAlignment(file, format, false, false);
}
- public void saveAlignment(String file, FileFormatI format, boolean stdout)
+ public void saveAlignment(String file, FileFormatI format, boolean stdout,
+ boolean forceBackup)
{
lastSaveSuccessful = true;
if (!stdout)
else
{
// create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled() && !stdout;
+ boolean doBackup = forceBackup
+ || (BackupFiles.getEnabled() && !stdout);
BackupFiles backupfiles = null;
if (doBackup)
{
if (Jalview.isHeadlessMode())
{
AnnotationLabels aal = getAlabels();
- int stringWidth = aal.drawLabels(null, false, idWidth, false, false, fm);
+ int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
+ fm);
idWidth = Math.max(idWidth, stringWidth);
}
else
throws ImageOutputException
{
makeAlignmentImage(type, file, renderer,
- BitmapImageSizing.nullBitmapImageSizing());
+ BitmapImageSizing.defaultBitmapImageSizing());
}
/**
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.io.File;
-import java.lang.reflect.InvocationTargetException;
import java.util.List;
import java.util.Locale;
import java.util.Map;
-import java.util.concurrent.Callable;
-import java.util.concurrent.CompletableFuture;
-import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.FutureTask;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
}
if (waitTotal > waitMax)
{
- jalview.bin.Console.errPrintln("Timed out waiting for Jmol to load files after "
- + waitTotal + "ms");
+ jalview.bin.Console.errPrintln(
+ "Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
// jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
// + "; files: " + files.toString());
@Override
public void makePDBImage(ImageMaker.TYPE type)
{
- try {
- makePDBImage(null, type, null,
- BitmapImageSizing.nullBitmapImageSizing());
- } catch (ImageOutputException ioex) {
- Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+ try
+ {
+ makePDBImage(null, type, null,
+ BitmapImageSizing.defaultBitmapImageSizing());
+ } catch (ImageOutputException ioex)
+ {
+ Console.error("Unexpected error whilst writing " + type.toString(),
+ ioex);
}
}
BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
userBis);
- float usescale = bis.scale;
- int usewidth = bis.width;
- int useheight = bis.height;
+ float usescale = bis.scale();
+ int usewidth = bis.width();
+ int useheight = bis.height();
ImageWriterI writer = new ImageWriterI()
{
.toLowerCase(Locale.ROOT);
final ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
-
+
final Throwable[] exceptions = new Throwable[1];
exceptions[0] = null;
final AppJmol us = this;
try
{
- Thread runner = Executors.defaultThreadFactory().newThread(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- exporter.doExport(file, us, width, height, view, renderer,
- userBis);
- } catch (Throwable t)
- {
- exceptions[0] = t;
- }
- }
- });
+ Thread runner = Executors.defaultThreadFactory()
+ .newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ exporter.doExport(file, us, width, height, view,
+ renderer, userBis);
+ } catch (Throwable t)
+ {
+ exceptions[0] = t;
+ }
+ }
+ });
runner.start();
- do { Thread.sleep(25); } while (runner.isAlive());
+ do
+ {
+ Thread.sleep(25);
+ } while (runner.isAlive());
} catch (Throwable e)
{
throw new ImageOutputException(
.openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Show Jmol help failed with: " + ex.getMessage());
+ jalview.bin.Console
+ .errPrintln("Show Jmol help failed with: " + ex.getMessage());
}
}
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import javax.swing.JTextField;
+import javax.swing.JTextPane;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.WindowConstants;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import javax.swing.text.JTextComponent;
import org.stackoverflowusers.file.WindowsShortcut;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.datamodel.Alignment;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
// used for jalviewjsTest
jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP");
}
+
}
/**
setKeyBindings(frame);
- // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
- int tries=3;
- boolean shown=false;
- Exception last=null;
+ // Since the latest FlatLaf patch, we occasionally have problems showing
+ // structureViewer frames...
+ int tries = 3;
+ boolean shown = false;
+ Exception last = null;
do
{
try
{
desktop.add(frame);
- shown=true;
+ shown = true;
} catch (IllegalArgumentException iaex)
{
- last=iaex;
+ last = iaex;
tries--;
- jalview.bin.Console.info(
- "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
- iaex);
+ jalview.bin.Console.info("Squashed IllegalArgument Exception ("
+ + tries + " left) for " + frame.getTitle(), iaex);
try
{
Thread.sleep(5);
} while (!shown && tries > 0);
if (!shown)
{
- jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+ jalview.bin.Console.error(
+ "Serious Problem whilst showing window " + frame.getTitle(),
+ last);
}
windowMenu.add(menuItem);
// this will run the shutdownHook but QuitHandler.getQuitResponse() should
// not run a second time if gotQuitResponse flag has been set (i.e. user
// confirmed quit of some kind).
- Jalview.exit("Desktop exiting.", 0);
+ Jalview.exit("Desktop exiting.", ExitCode.OK);
}
private void storeLastKnownDimensions(String string, Rectangle jc)
}
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Error opening help: " + ex.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error opening help: " + ex.getMessage());
}
}
boolean autoSave = projectFile != null && !saveAs
&& BackupFiles.getEnabled();
- // jalview.bin.Console.outPrintln("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // jalview.bin.Console.outPrintln("autoSave="+autoSave+",
+ // projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
Desktop us = Desktop.instance;
Desktop.instance = null;
// call dispose in a separate thread - try to avoid indirect deadlocks
- new Thread(new Runnable() {
+ new Thread(new Runnable()
+ {
@Override
public void run()
{
ExecutorService dex = us.dialogExecutor;
- if (dex!=null) {
+ if (dex != null)
+ {
dex.shutdownNow();
- us.dialogExecutor=null;
+ us.dialogExecutor = null;
us.block.drainPermits();
}
us.dispose();
alignFrameModalMap.remove(af);
}
+ public void nonBlockingDialog(String title, String message, String button,
+ int type, boolean scrollable, boolean modal)
+ {
+ nonBlockingDialog(32, 2, title, message, null, button, type, scrollable,
+ false, modal);
+ }
+
+ public void nonBlockingDialog(int width, int height, String title,
+ String message, String boxtext, String button, int type,
+ boolean scrollable, boolean html, boolean modal)
+ {
+ if (type < 0)
+ {
+ type = JvOptionPane.WARNING_MESSAGE;
+ }
+ JLabel jl = new JLabel(message);
+
+ JTextComponent jtc = null;
+ if (html)
+ {
+ JTextPane jtp = new JTextPane();
+ jtp.setContentType("text/html");
+ jtp.setEditable(false);
+ jtp.setAutoscrolls(true);
+ jtp.setText(boxtext);
+
+ jtc = jtp;
+ }
+ else
+ {
+ JTextArea jta = new JTextArea(height, width);
+ // jta.setLineWrap(true);
+ jta.setEditable(false);
+ jta.setWrapStyleWord(true);
+ jta.setAutoscrolls(true);
+ jta.setText(boxtext);
+
+ jtc = jta;
+ }
+
+ JScrollPane jsp = scrollable
+ ? new JScrollPane(jtc, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+ JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
+ : null;
+
+ JvOptionPane jvp = JvOptionPane.newOptionDialog(this);
+
+ JPanel jp = new JPanel();
+ jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS));
+
+ if (message != null)
+ {
+ jl.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jl);
+ }
+ if (boxtext != null)
+ {
+ if (scrollable)
+ {
+ jsp.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jsp);
+ }
+ else
+ {
+ jtc.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jp.add(jtc);
+ }
+ }
+
+ jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
+ });
+ jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type,
+ null, new Object[]
+ { button }, button, modal, null, false);
+ }
+
}
String imageSource) throws ImageOutputException
{
doExport(file, parent, width, height, imageSource, null,
- BitmapImageSizing.nullBitmapImageSizing());
+ BitmapImageSizing.defaultBitmapImageSizing());
}
public void doExport(File file, Component parent, int width, int height,
private static void outputMessage(Object message)
{
- jalview.bin.Console.outPrintln(">>> JOption Message : " + message.toString());
+ jalview.bin.Console
+ .outPrintln(">>> JOption Message : " + message.toString());
}
public static Object getMockResponse()
int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
Object initialValue, boolean modal, JButton[] buttons)
{
+ showDialogOnTopAsync(dialogParent, label, actionString,
+ JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+ initialValue, modal, buttons, true);
+ }
+
+ public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+ String actionString, int JOPTIONPANE_OPTION,
+ int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+ Object initialValue, boolean modal, JButton[] buttons,
+ boolean dispose)
+ {
if (!isInteractiveMode())
{
handleResponse(getMockResponse());
JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
buttons);
- dialogParent.setAlwaysOnTop(false);
- dialogParent.dispose();
+ if (dispose)
+ {
+ dialogParent.setAlwaysOnTop(false);
+ dialogParent.dispose();
+ }
}
/**
import com.stevesoft.pat.Regex;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
{
c.setRight(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (BinaryNode) c.right();
+ c = c.right();
}
else
{
c.setLeft(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (BinaryNode) c.left();
+ c = c.left();
}
if (realroot == null)
// Just advance focus, if we need to
if ((c.left() != null) && (!c.left().isLeaf()))
{
- c = (BinaryNode) c.left();
+ c = c.left();
}
}
}
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+ root = root.right().detach(); // remove the imaginary root.
if (!RootHasDistance)
{
if (args == null || args.length != 1)
{
Jalview.exit(
- "Takes one argument - file name of a newick tree file.", 0);
+ "Takes one argument - file name of a newick tree file.",
+ ExitCode.INVALID_ARGUMENT);
}
File fn = new File(args[0]);
jalview.bin.Console.outPrintln("Original file :\n");
Regex nonl = new Regex("\n+", "");
- jalview.bin.Console.outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
+ jalview.bin.Console
+ .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
jalview.bin.Console.outPrintln("Parsed file.\n");
- jalview.bin.Console.outPrintln("Default output type for original input.\n");
+ jalview.bin.Console
+ .outPrintln("Default output type for original input.\n");
jalview.bin.Console.outPrintln(trf.print());
jalview.bin.Console.outPrintln("Without bootstraps.\n");
jalview.bin.Console.outPrintln(trf.print(false));
jalview.bin.Console.outPrintln("Without distances.\n");
jalview.bin.Console.outPrintln(trf.print(true, false));
- jalview.bin.Console.outPrintln("Without bootstraps but with distanecs.\n");
+ jalview.bin.Console
+ .outPrintln("Without bootstraps but with distanecs.\n");
jalview.bin.Console.outPrintln(trf.print(false, true));
jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n");
jalview.bin.Console.outPrintln(trf.print(false, false));
- jalview.bin.Console.outPrintln("With bootstraps and with distances.\n");
+ jalview.bin.Console
+ .outPrintln("With bootstraps and with distances.\n");
jalview.bin.Console.outPrintln(trf.print(true, true));
} catch (java.io.IOException e)
{
import java.io.PrintStream;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
public class AWTConsole extends WindowAdapter
implements WindowListener, ActionListener, Runnable
} catch (Exception e)
{
}
- Jalview.exit("Window closing. Bye!", 0);
+ Jalview.exit("Window closing. Bye!", ExitCode.OK);
}
@Override
boolean allowSingleFilenameThatDoesNotExist)
{
pattern = substituteHomeDir(pattern);
+ String relativePattern = pattern.startsWith(File.separator) ? null
+ : pattern;
List<File> files = new ArrayList<>();
/*
* For efficiency of the Files.walkFileTree(), let's find the longest path that doesn't need globbing.
{
String pS = pattern.substring(0, lastFS + 1);
String rest = pattern.substring(lastFS + 1);
- Path parentDir = Paths.get(pS).toAbsolutePath();
+ if ("".equals(pS))
+ {
+ pS = ".";
+ }
+ Path parentDir = Paths.get(pS);
if (parentDir.toFile().exists())
{
try
return null;
String dirname = null;
- try
- {
- File p = file.getParentFile();
- File d = new File(substituteHomeDir(p.getPath()));
- dirname = d.getCanonicalPath();
- } catch (IOException e)
+ File p = file.getParentFile();
+ if (p == null)
{
- Console.debug(
- "Exception when getting dirname of '" + file.getPath() + "'",
- e);
- dirname = "";
+ p = new File(".");
}
+ File d = new File(substituteHomeDir(p.getPath()));
+ dirname = d.getPath();
return dirname;
}
+
+ public static String convertWildcardsToPath(String value, String wildcard,
+ String dirname, String basename)
+ {
+ if (value == null)
+ {
+ return null;
+ }
+ StringBuilder path = new StringBuilder();
+ int lastFileSeparatorIndex = value.lastIndexOf(File.separatorChar);
+ int wildcardBeforeIndex = value.indexOf(wildcard);
+ if (lastFileSeparatorIndex > wildcard.length() - 1
+ && wildcardBeforeIndex < lastFileSeparatorIndex)
+ {
+ path.append(value.substring(0, wildcardBeforeIndex));
+ path.append(dirname);
+ path.append(value.substring(wildcardBeforeIndex + wildcard.length(),
+ lastFileSeparatorIndex + 1));
+ }
+ else
+ {
+ path.append(value.substring(0, lastFileSeparatorIndex + 1));
+ }
+ int wildcardAfterIndex = value.indexOf(wildcard,
+ lastFileSeparatorIndex);
+ if (wildcardAfterIndex > lastFileSeparatorIndex)
+ {
+ path.append(value.substring(lastFileSeparatorIndex + 1,
+ wildcardAfterIndex));
+ path.append(basename);
+ path.append(value.substring(wildcardAfterIndex + wildcard.length()));
+ }
+ else
+ {
+ path.append(value.substring(lastFileSeparatorIndex + 1));
+ }
+ return path.toString();
+ }
+
+ public static File getParentDir(File file)
+ {
+ if (file == null)
+ {
+ return null;
+ }
+ File parentDir = file.getAbsoluteFile().getParentFile();
+ return parentDir;
+ }
+
+ public static boolean checkParentDir(File file, boolean mkdirs)
+ {
+ if (file == null)
+ {
+ return false;
+ }
+ File parentDir = getParentDir(file);
+ if (parentDir.exists())
+ {
+ // already exists, nothing to do so nothing to worry about!
+ return true;
+ }
+
+ if (!mkdirs)
+ {
+ return false;
+ }
+
+ Path path = file.toPath();
+ for (int i = 0; i < path.getNameCount(); i++)
+ {
+ Path p = path.getName(i);
+ if ("..".equals(p.toString()))
+ {
+ Console.warn("Cautiously not running mkdirs on " + file.toString()
+ + " because the path to be made contains '..'");
+ return false;
+ }
+ }
+
+ return parentDir.mkdirs();
+ }
}
BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
userBis);
- float usescale = bis.scale;
- int usewidth = bis.width;
- int useheight = bis.height;
+ float usescale = bis.scale();
+ int usewidth = bis.width();
+ int useheight = bis.height();
bi = new BufferedImage(usewidth, useheight, BufferedImage.TYPE_INT_RGB);
graphics = bi.getGraphics();
}
/**
- * Takes suggested float scale, int width, int height and create a bounding
- * box returned as a BitmapImageSizing object with consistent scale, width,
- * height fields.
+ * Takes initial width and height, and suggested float scale, int width, int
+ * height and create a bounding box returned as a BitmapImageSizing object
+ * with consistent scale, width, height fields.
*
+ * @param width
+ * The unscaled image width
+ * @param height
+ * The unscaled image height
* @param scale
+ * The suggested scaling
* @param bitmapwidth
+ * The suggested width
* @param bitmapheight
- * @return BitmapImageSizing
+ * The suggested height
+ * @return BitmapImageSizing A consistent scale,width and height for the final
+ * image
*/
public static BitmapImageSizing getScaleWidthHeight(int width, int height,
float scale, int bitmapwidth, int bitmapheight)
int usewidth = width;
int useheight = height;
+ if ((width == 0 && bitmapwidth > 0)
+ || (height == 0 && bitmapheight > 0))
+ {
+ // original image is zero sized! Avoid dividing by zero!
+ return BitmapImageSizing.nullBitmapImageSizing();
+ }
+
// use the smallest positive scale (i.e. fit in the box)
if (scale > 0.0f)
{
useheight = bitmapheight;
}
}
- return new BitmapImageSizing(usescale, usewidth, useheight);
+ return new BitmapImageSizing(usescale, usewidth, useheight, false);
}
/**
public static BitmapImageSizing getScaleWidthHeight(int width, int height,
BitmapImageSizing bis)
{
- return ImageMaker.getScaleWidthHeight(width, height, bis.scale,
- bis.width, bis.height);
+ return ImageMaker.getScaleWidthHeight(width, height, bis.scale(),
+ bis.width(), bis.height());
}
/**
public static BitmapImageSizing parseScaleWidthHeightStrings(
String scaleS, String widthS, String heightS)
{
+ if (scaleS == null && widthS == null && heightS == null)
+ {
+ // if all items are null (i.e. not provided) we use the dynamic
+ // preferences set BIS
+ return BitmapImageSizing.defaultBitmapImageSizing();
+ }
+
float scale = 0.0f;
int width = 0;
int height = 0;
}
}
- return new BitmapImageSizing(scale, width, height);
+ return new BitmapImageSizing(scale, width, height, false);
}
}
public class BitmapImageSizing
{
- public final float scale;
+ private final float scale;
- public final int width;
+ private final int width;
- public final int height;
+ private final int height;
- public BitmapImageSizing(float scale, int width, int height)
+ private boolean isDefault = false;
+
+ public BitmapImageSizing(float scale, int width, int height,
+ boolean isDefault)
{
this.scale = scale;
this.width = width;
this.height = height;
+ this.isDefault = isDefault;
+ }
+
+ public boolean isNull()
+ {
+ return scale == 0.0f && width == 0 && height == 0;
}
public static BitmapImageSizing nullBitmapImageSizing()
{
- return new BitmapImageSizing(0.0f, 0, 0);
+ return new BitmapImageSizing(0.0f, 0, 0, false);
}
-
+
public static final String BITMAP_SCALE = "BITMAP_SCALE";
public static final String BITMAP_HEIGHT = "BITMAP_HEIGHT";
*/
public static BitmapImageSizing defaultBitmapImageSizing()
{
-
- return new BitmapImageSizing(Cache.getDefault(BITMAP_SCALE,0)/10f,Cache.getDefault(BITMAP_WIDTH,0),Cache.getDefault(BITMAP_HEIGHT,0));
-
+ return new BitmapImageSizing(0f, 0, 0, true);
+ }
+
+ private float defaultScale()
+ {
+ return Cache.getDefault(BITMAP_SCALE, 0f);
+ }
+
+ private int defaultWidth()
+ {
+ return Cache.getDefault(BITMAP_WIDTH, 0);
+ }
+
+ private int defaultHeight()
+ {
+ return Cache.getDefault(BITMAP_HEIGHT, 0);
+ }
+
+ public float scale()
+ {
+ return isDefault() ? defaultScale() : scale;
+ }
+
+ public int width()
+ {
+ return isDefault() ? defaultWidth() : width;
+ }
+
+ public int height()
+ {
+ return isDefault() ? defaultHeight() : height;
+ }
+
+ public boolean isDefault()
+ {
+ return isDefault;
}
}
}
}
+ private final String deleteDir = "test/deleteAfter";
+
@Test(
groups = "Functional",
dataProvider = "allLinkedIdsData",
"File " + nonfilename + " exists when it shouldn't!");
}
}
+
+ File deleteDirF = new File(deleteDir);
+ if (deleteDirF.exists())
+ {
+ deleteDirF.delete();
+ }
}
@DataProvider(name = "allLinkedIdsData")
{
return new Object[][] {
//
- /*
- */
{ "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
null },
- { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
null },
- { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+ // --mkdirs
+ { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
+ + deleteDir
+ + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
+ + deleteDir
+ + "/{dirname}/{basename}.aln --close --all --mkdirs",
+ new String[]
+ { deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ "test/jalview/bin/argparser/testfiles/test1.aln",
+ "test/jalview/bin/argparser/testfiles/test2.aln",
+ "test/jalview/bin/argparser/testfiles/test3.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
//
};
}
String jvmArgs = HiDPISetting.getScalePropertyArg(scale);
- String appArgs = " -open examples/uniref50.fa -nosplash -nonews -noquestionnaire -nousagestats -nowebservicediscovery";
+ String appArgs = " --open examples/uniref50.fa --nosplash --nonews --noquestionnaire --nousagestats --nowebservicediscovery";
Worker worker = getJalviewDesktopRunner(jvmArgs, appArgs);
assertNotNull(worker, "worker is null");
{
while ((ln = worker.getErrorReader().readLine()) != null)
{
- if (++count > 100)
+ if (++count > 150)
{
break;
}
}
@Test(groups = "Functional", dataProvider = "allLinkedIdsData")
- public void allLinkedIdsTest(String commandLineArgs, Arg a,
+ public void allLinkedIdsTest(String pwd, String commandLineArgs, Arg a,
String[] values, String[] nonvalues)
{
+ String userDir = System.getProperty("user.dir");
+ if (pwd != null)
+ {
+ File pwdFile = new File(pwd);
+ System.setProperty("user.dir", pwdFile.getAbsolutePath());
+ }
String[] args = commandLineArgs.split("\\s+");
ArgParser argparser = new ArgParser(args);
ArgValues avs = avm.getArgValues(a);
ArgValue av = avs.getArgValue();
String v = av.getValue();
- value = new File(value).getAbsolutePath();
+ value = new File(value).getPath();
Assert.assertEquals(v, value, "Arg value for " + a.argString()
+ " not applied correctly to linkedId '" + linkedId + "'");
}
}
+ System.setProperty("user.dir", userDir);
}
@DataProvider(name = "allLinkedIdsData")
//
/*
*/
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
Arg.CLOSE, new String[]
{ null, null, null },
null },
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
Arg.OUTPUT, new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/test3.stk", },
null },
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
Arg.IMAGE, new String[]
{ "test/jalview/bin/argparser/testfiles/test1.png",
"test/jalview/bin/argparser/testfiles/test2.png",
"test/jalview/bin/argparser/testfiles/test3.png", },
null },
+ /*
+ * Find a way to change pwd reliably -- need to match "*.fa" against some files!
+ { "test/jalview/bin/argparser/testfiles",
+
+ "--open=*.fa --image={dirname}/{basename}.png --close",
+ Arg.IMAGE, new String[]
+ { "./test1.png", "./test2.png", "./test3.png", }, null },
+ */
//
};
}
};
}
-}
+}
\ No newline at end of file
package jalview.util;
import java.io.File;
-import java.io.IOException;
import java.util.List;
import org.testng.Assert;
}
@Test(groups = "Functional", dataProvider = "dirnamesAndBasenames")
- public void testDirnamesAndBasenames(String filename, int where,
- String dirname, String basename, String notInDirname)
+ public void testDirnamesAndBasenames(String filename, String dirname,
+ String endsWith, String basename, String notInDirname)
{
File file = new File(filename);
String d = FileUtils.getDirname(file);
String b = FileUtils.getBasename(file);
Assert.assertEquals(b, basename);
- if (where == 0)
- Assert.assertEquals(d, dirname);
- else if (where < 0)
- Assert.assertTrue(d.startsWith(dirname),
- "getDirname(" + file.getPath() + ")=" + d
- + " didn't start with '" + dirname + "'");
- else if (where > 0)
- Assert.assertTrue(d.endsWith(dirname), "getDirname(" + file.getPath()
- + ")=" + d + " didn't end with '" + d + "'");
+ Assert.assertTrue(d.startsWith(dirname), "getDirname(" + file.getPath()
+ + ")=" + d + " didn't start with '" + dirname + "'");
+ Assert.assertTrue(d.endsWith(endsWith), "getDirname(" + file.getPath()
+ + ")=" + d + " didn't end with '" + endsWith + "'");
// ensure dirname doesn't end with basename (which means you can't use same
// filename as dir in tests!)
- Assert.assertFalse(d.endsWith(b));
+ Assert.assertFalse(d.endsWith(b), "Processed dirname '" + d
+ + "' ends with '" + b + "' when it shouldn't");
if (notInDirname != null)
- Assert.assertFalse(d.contains(notInDirname));
+ Assert.assertFalse(d.contains(notInDirname), "Processed directory '"
+ + d + "' contains '" + notInDirname + "' when it shouldn't");
}
@DataProvider(name = "patternsAndMinNumFiles")
@DataProvider(name = "dirnamesAndBasenames")
public Object[][] dirnamesAndBasenames()
{
- String homeDir = null;
- try
- {
- homeDir = new File(System.getProperty("user.home"))
- .getCanonicalPath();
- } catch (IOException e)
- {
- System.err.println("Problem getting canonical home dir");
- e.printStackTrace();
- }
+ String homeDir = new File(System.getProperty("user.home")).getPath();
return new Object[][] { // -1=startsWith, 0=equals, 1=endsWith
- { "~/hello/sailor", -1, homeDir, "sailor", "~" }, //
- { "~/hello/sailor", 1, "/hello", "sailor", "~" }, //
- { "./examples/uniref50.fa", -1, "/", "uniref50", "." }, //
- { "./examples/uniref50.fa", 1, "/examples", "uniref50", "." }, //
- { "examples/uniref50.fa", 1, "/examples", "uniref50", ".fa" }, //
+ { "~/hello/sailor", homeDir, "/hello", "sailor", "~" }, //
+ { "./examples/uniref50.fa", "./", "examples", "uniref50", "Users" }, //
+ { "./examples/uniref50.1.fa", "./", "examples", "uniref50.1",
+ "Users" }, //
+ { "examples/uniref50.fa", "examples", "examples", "uniref50",
+ ".fa" }, //
};
}
+
+ @Test(groups = "Functional", dataProvider = "convertWildcardsToPathData")
+ public void convertWildcardsToPathTest(String value, String wildcard,
+ String dirname, String basename, String path)
+ {
+
+ Assert.assertEquals(
+ FileUtils.convertWildcardsToPath(value, wildcard, dirname,
+ basename),
+ path, "Conversion of wildcard output path is not right.");
+
+ }
+
+ @DataProvider(name = "convertWildcardsToPathData")
+ public Object[][] convertWildcardsToPathData()
+ {
+ return new Object[][] {
+ /*
+ * cmdline args
+ * Arg (null if only testing headless)
+ * String value if there is one (null otherwise)
+ * boolean value if String value is null
+ * expected value of isHeadless()
+ */
+ /*
+ */
+ { "*/*", "*", "{dirname}", "{basename}", "{dirname}/{basename}" },
+ { "*/", "*", "{dirname}", "{basename}", "{dirname}/" },
+ { "/*", "*", "{dirname}", "{basename}", "/{basename}" },
+ { "*", "*", "{dirname}", "{basename}", "{basename}" },
+ { "tmp/output/*/file-*.stk", "*", "{dirname}", "{basename}",
+ "tmp/output/{dirname}/file-{basename}.stk" },
+ { "/*.file", "*", "{dirname}", "{basename}", "/{basename}.file" },
+ { "*/file.stk", "*", "{dirname}", "{basename}",
+ "{dirname}/file.stk" },
+ { "tmp/abc*def/file.stk", "*", "{dirname}", "{basename}",
+ "tmp/abc{dirname}def/file.stk" },
+ { "a*b/c*d", "*", "{dirname}", "{basename}",
+ "a{dirname}b/c{basename}d" },
+ { "a*b/c", "*", "{dirname}", "{basename}", "a{dirname}b/c" },
+ { "a/b*c", "*", "{dirname}", "{basename}", "a/b{basename}c" },
+ { "a*b", "*", "{dirname}", "{basename}", "a{basename}b" },
+ { "aSTARb/cSTARd", "STAR", "BEFORE", "AFTER", "aBEFOREb/cAFTERd" },
+ { "aSTARb/c", "STAR", "BEFORE", "AFTER", "aBEFOREb/c" },
+ { "a/bSTARc", "STAR", "BEFORE", "AFTER", "a/bAFTERc" },
+ { "aSTARb", "STAR", "BEFORE", "AFTER", "aAFTERb" },
+ //
+ };
+ }
+
}
--- /dev/null
+package jalview.util;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.util.imagemaker.BitmapImageSizing;
+
+public class ImageMakerTest
+{
+ @Test(groups = { "Functional" })
+ public void testParseScaleWidthHeightStrings()
+ {
+ Cache.setPropsAreReadOnly(true);
+ Cache.loadProperties("test/jalview/bin/testProps.jvprops");
+
+ Cache.removeProperty(BitmapImageSizing.BITMAP_SCALE);
+ Cache.removeProperty(BitmapImageSizing.BITMAP_HEIGHT);
+ Cache.removeProperty(BitmapImageSizing.BITMAP_WIDTH);
+
+ BitmapImageSizing bis = null;
+
+ // No defaults set, 3 values given. Should be the 3 values.
+ bis = ImageMaker.parseScaleWidthHeightStrings("1.2", "3", "4");
+ Assert.assertEquals(bis.scale(), 1.2f,
+ "scale not parsed and set to value given");
+ Assert.assertEquals(bis.width(), 3,
+ "width not parsed and set to value given");
+ Assert.assertEquals(bis.height(), 4,
+ "height not parsed and set to value given");
+
+ // No defaults set, 1 value given. Should be the 1 value and 2 0s.
+ bis = ImageMaker.parseScaleWidthHeightStrings("1.2", null, null);
+ Assert.assertEquals(bis.scale(), 1.2f,
+ "scale not parsed and set to value given");
+ Assert.assertEquals(bis.width(), 0, "width not parsed and set to 0");
+ Assert.assertEquals(bis.height(), 0, "height not parsed and set to 0");
+
+ // No defaults set, 1 value given. Should be the 1 value and 2 0s. (checking
+ // the other value)
+ bis = ImageMaker.parseScaleWidthHeightStrings(null, "1", null);
+ Assert.assertEquals(bis.scale(), 0f, "scale not parsed and set to 0f");
+ Assert.assertEquals(bis.width(), 1,
+ "width not parsed and set to value given");
+ Assert.assertEquals(bis.height(), 0, "height not parsed and set to 0");
+
+ // No defaults set, no values given, these should first look at defaults and
+ // then set all to 0
+ bis = ImageMaker.parseScaleWidthHeightStrings(null, null, null);
+ Assert.assertEquals(bis.scale(), 0f,
+ "scale not parsed and set to undefined default 0f");
+ Assert.assertEquals(bis.width(), 0,
+ "width not parsed and set to undefined default 0");
+ Assert.assertEquals(bis.height(), 0,
+ "height not parsed and set to undefined default 0");
+
+ Cache.setProperty(BitmapImageSizing.BITMAP_HEIGHT, "1");
+ // 1 default set, bis should detect this
+ Assert.assertEquals(bis.scale(), 0f,
+ "scale not parsed and set to undefined default 0f");
+ Assert.assertEquals(bis.width(), 0,
+ "width not parsed and set to undefined default 0");
+ Assert.assertEquals(bis.height(), 1,
+ "height not parsed and set to default 1");
+
+ Cache.setProperty(BitmapImageSizing.BITMAP_SCALE, "3.4");
+ Cache.setProperty(BitmapImageSizing.BITMAP_WIDTH, "2");
+ // Now all 3 defaults set, bis should detect this
+ Assert.assertEquals(bis.scale(), 3.4f,
+ "scale not parsed and set to undefined default 3.2f");
+ Assert.assertEquals(bis.width(), 2,
+ "width not parsed and set to undefined default 2");
+ Assert.assertEquals(bis.height(), 1,
+ "height not parsed and set to default 1");
+
+ // 3 defaults set, and 3 values given, should use the 3 values
+ bis = ImageMaker.parseScaleWidthHeightStrings("1.2", "3", "4");
+ Assert.assertEquals(bis.scale(), 1.2f,
+ "scale not parsed and set to value given");
+ Assert.assertEquals(bis.width(), 3,
+ "width not parsed and set to value given");
+ Assert.assertEquals(bis.height(), 4,
+ "height not parsed and set to value given");
+
+ // 3 defaults set, and 1 value given, should use the 1 value and 2 0s
+ bis = ImageMaker.parseScaleWidthHeightStrings("1.2", null, null);
+ Assert.assertEquals(bis.scale(), 1.2f,
+ "scale not parsed and set to value given");
+ Assert.assertEquals(bis.width(), 0,
+ "width not parsed and set to undefined 0");
+ Assert.assertEquals(bis.height(), 0,
+ "height not parsed and set to undefined 0");
+
+ // 3 defaults set, and 1 value given, should use the 1 value and 2 0s
+ bis = ImageMaker.parseScaleWidthHeightStrings(null, null, "5");
+ Assert.assertEquals(bis.scale(), 0f,
+ "scale not parsed and set to undefined 0f");
+ Assert.assertEquals(bis.width(), 0,
+ "width not parsed and set to undefined 0");
+ Assert.assertEquals(bis.height(), 5,
+ "height not parsed and set to value given");
+
+ // 3 defaults set, and no values given, should use the 3 default values
+ bis = ImageMaker.parseScaleWidthHeightStrings(null, null, null);
+ Assert.assertEquals(bis.scale(), 3.4f,
+ "scale not parsed and set to undefined default 3.2f");
+ Assert.assertEquals(bis.width(), 2,
+ "width not parsed and set to undefined default 2");
+ Assert.assertEquals(bis.height(), 1,
+ "height not parsed and set to default 1");
+ }
+}
import jalview.bin.Cache;
-public class BitmapImageSizeTest {
- @Test(groups = {"Functional"})
- public void testCacheSettingsRecovery() {
+public class BitmapImageSizeTest
+{
+ @Test(groups = { "Functional" })
+ public void testCacheSettingsRecovery()
+ {
Cache.setPropsAreReadOnly(true);
Cache.loadProperties("test/jalview/bin/testProps.jvprops");
-
+
Cache.removeProperty(BitmapImageSizing.BITMAP_HEIGHT);
Cache.removeProperty(BitmapImageSizing.BITMAP_SCALE);
Cache.removeProperty(BitmapImageSizing.BITMAP_WIDTH);
-
+
BitmapImageSizing def = BitmapImageSizing.defaultBitmapImageSizing();
BitmapImageSizing zero = BitmapImageSizing.nullBitmapImageSizing();
- assertEquals(def.height, zero.height);
- assertEquals(def.width, zero.width);
- assertEquals(def.scale, zero.scale);
-
- Cache.setProperty(BitmapImageSizing.BITMAP_HEIGHT,"120");
- Cache.setProperty(BitmapImageSizing.BITMAP_SCALE,"240");
- Cache.setProperty(BitmapImageSizing.BITMAP_WIDTH,"360");
-
- def = BitmapImageSizing.defaultBitmapImageSizing();
-
- assertEquals(def.height, 120);
- assertEquals(def.width, 360);
- assertEquals(def.scale, 24f);
-
+ assertEquals(def.height(), zero.height());
+ assertEquals(def.width(), zero.width());
+ assertEquals(def.scale(), zero.scale());
+
+ Cache.setProperty(BitmapImageSizing.BITMAP_HEIGHT, "120");
+ Cache.setProperty(BitmapImageSizing.BITMAP_SCALE, "24");
+ Cache.setProperty(BitmapImageSizing.BITMAP_WIDTH, "360");
+
+ // default now updates dynamically
+ // def = BitmapImageSizing.defaultBitmapImageSizing();
+
+ assertEquals(def.height(), 120);
+ assertEquals(def.width(), 360);
+ assertEquals(def.scale(), 24f);
+
Cache.removeProperty(BitmapImageSizing.BITMAP_WIDTH);
-
- def = BitmapImageSizing.defaultBitmapImageSizing();
- assertEquals(def.height, 120);
- assertEquals(def.width, zero.width);
- assertEquals(def.scale, 24f);
+
+ // def = BitmapImageSizing.defaultBitmapImageSizing();
+ assertEquals(def.height(), 120);
+ assertEquals(def.width(), zero.width());
+ assertEquals(def.scale(), 24f);
}
}
git://source.jalview.org / jalview.git / commitdiff