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Cleanup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@205 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-26 21:24:12 +00:00
parent 728f932ecf
commit f7097c8ee7
1 changed files with 24 additions and 12 deletions
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42
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
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@ -356,7 +356,7 @@ public class ArgumentParser {
* will be alone a set. Every option should appear in exactly one set. * will be alone a set. Every option should appear in exactly one set.
* WARNING: Has no concept of nested dependencies. * WARNING: Has no concept of nested dependencies.
* @param fields list of fields for which to check options. * @param fields list of fields for which to check options.
* @return * @return groupings of mutually exclusive options.
*/ */
private List<Set<Field>> groupExclusiveOptions( Field[] fields ) { private List<Set<Field>> groupExclusiveOptions( Field[] fields ) {
List<Set<Field>> optionGroups = new ArrayList<Set<Field>>(); List<Set<Field>> optionGroups = new ArrayList<Set<Field>>();
@ -414,30 +414,42 @@ public class ArgumentParser {
String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1); String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1);
if(shortName.length() != 1) if(shortName.length() != 1)
throw new IllegalArgumentException("Invalid short name: " + shortName); throw new IllegalArgumentException("Invalid short name: " + shortName);
String description = argument.doc();
boolean isRequired = argument.required();
boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE); boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE);
boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType()); boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType());
if( isFlag && isCollection ) if( isFlag && isCollection )
throw new IllegalArgumentException("Can't have an array of flags."); throw new IllegalArgumentException("Can't have an array of flags.");
String description = String.format("[%s] %s", sourceName, argument.doc()); OptionBuilder.withLongOpt(fullName);
OptionBuilder ob = OptionBuilder.withLongOpt(fullName);
if( !isFlag ) { if( !isFlag ) {
ob = ob.withArgName(fullName); OptionBuilder.withArgName(fullName);
ob = isCollection ? ob.hasArgs() : ob.hasArg(); if( isCollection )
OptionBuilder.hasArgs();
else
OptionBuilder.hasArg();
} }
if( argument.required() ) { if( isRequired ) {
ob = ob.isRequired(); OptionBuilder.isRequired();
description = String.format("[%s] (Required Option) %s", sourceName, argument.doc()); description = String.format("(Required Option) %s", description);
}
if( description.length() != 0 ) ob = ob.withDescription( description );
Option option = ob.create( shortName );
return option;
} }
sourceName = sourceName.trim();
if( sourceName.length() > 0 )
description = String.format("[%s] %s", sourceName, description );
if( description.length() != 0 ) OptionBuilder.withDescription( description );
return OptionBuilder.create( shortName );
}
/**
* Constructs a command-line argument given a string and field.
* @param f Field type from which to infer the type.
* @param strs Collection of parameter strings to parse.
* @return Parsed object of the inferred type.
*/
private Object constructFromString(Field f, String[] strs) { private Object constructFromString(Field f, String[] strs) {
Class type = f.getType(); Class type = f.getType();