/**
* Gets a detailed description for a given argument group.
*
* @param argumentDefinitionGroup The group of argument definitions to render.
* @return A string giving detailed info about the contents of this group.
*/
private String getDetailForGroup(ArgumentDefinitionGroup argumentDefinitionGroup) {
if (argumentDefinitionGroup.allHidden()) return "";
StringBuilder builder = new StringBuilder();
Formatter formatter = new Formatter(builder);
if (argumentDefinitionGroup.groupName != null
&& argumentDefinitionGroup.argumentDefinitions.size() != 0)
builder.append(String.format("%nArguments for %s:%n", argumentDefinitionGroup.groupName));
List<ArgumentDefinition> argumentDefinitions = new ArrayList<ArgumentDefinition>();
for (ArgumentDefinition argumentDefinition : argumentDefinitionGroup.argumentDefinitions) {
if (!argumentDefinition.isHidden) argumentDefinitions.add(argumentDefinition);
}
// Try to fit the entire argument definition across the screen, but impose an arbitrary cap of
// 3/4 *
// LINE_WIDTH in case the length of the arguments gets out of control.
int argWidth =
Math.min(
findLongestArgumentCallingInfo(argumentDefinitions),
(TextFormattingUtils.DEFAULT_LINE_WIDTH * 3) / 4 - FIELD_SEPARATION_WIDTH);
int docWidth = TextFormattingUtils.DEFAULT_LINE_WIDTH - argWidth - FIELD_SEPARATION_WIDTH;
for (ArgumentDefinition argumentDefinition : argumentDefinitions) {
Iterator<String> wordWrappedArgs =
TextFormattingUtils.wordWrap(getArgumentCallingInfo(argumentDefinition), argWidth)
.iterator();
Iterator<String> wordWrappedDoc =
TextFormattingUtils.wordWrap(getArgumentDoc(argumentDefinition), docWidth).iterator();
while (wordWrappedArgs.hasNext() || wordWrappedDoc.hasNext()) {
String arg = wordWrappedArgs.hasNext() ? wordWrappedArgs.next() : "";
String doc = wordWrappedDoc.hasNext() ? wordWrappedDoc.next() : "";
String formatString = "%-" + argWidth + "s%" + FIELD_SEPARATION_WIDTH + "s%s%n";
formatter.format(formatString, arg, "", doc);
}
}
return builder.toString();
}
/**
* Creates a program record (@PG) tag
*
* @param toolkit the engine
* @param walker the walker object (so we can extract the command line)
* @param PROGRAM_RECORD_NAME the name for the PG tag
* @return a program record for the tool
*/
public static SAMProgramRecord createProgramRecord(
GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
try {
final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version");
programRecord.setProgramVersion(version);
} catch (MissingResourceException e) {
// couldn't care less if the resource is missing...
}
programRecord.setCommandLine(
toolkit.createApproximateCommandLineArgumentString(toolkit, walker));
return programRecord;
}
/**
* Gets the synopsis: the actual command to run.
*
* @param runningInstructions Instructions on how to run hte application.
* @param argumentGroups Program arguments sorted in order of definition group displays.
* @return A synopsis line.
*/
private String getSynopsis(
String runningInstructions, List<ArgumentDefinitionGroup> argumentGroups) {
// Build out the synopsis all as one long line.
StringBuilder lineBuilder = new StringBuilder();
Formatter lineFormatter = new Formatter(lineBuilder);
lineFormatter.format("java %s", runningInstructions);
for (ArgumentDefinitionGroup argumentGroup : argumentGroups) {
for (ArgumentDefinition argumentDefinition : argumentGroup.argumentDefinitions) {
if (argumentDefinition.isHidden) continue;
lineFormatter.format(" ");
if (!argumentDefinition.required) lineFormatter.format("[");
if (argumentDefinition.shortName != null)
lineFormatter.format("-%s", argumentDefinition.shortName);
else lineFormatter.format("--%s", argumentDefinition.fullName);
if (!argumentDefinition.isFlag) lineFormatter.format(" <%s>", argumentDefinition.fullName);
if (!argumentDefinition.required) lineFormatter.format("]");
}
}
// Word wrap the synopsis.
List<String> wrappedSynopsis =
TextFormattingUtils.wordWrap(
lineBuilder.toString(), TextFormattingUtils.DEFAULT_LINE_WIDTH);
String header = "usage: ";
int headerLength = header.length();
StringBuilder synopsisBuilder = new StringBuilder();
Formatter synopsisFormatter = new Formatter(synopsisBuilder);
for (String synopsisLine : wrappedSynopsis) {
synopsisFormatter.format("%" + headerLength + "s%s%n", header, synopsisLine);
header = "";
}
return synopsisBuilder.toString();
}