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Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-24 19:44:04 +00:00
parent e2ec703a32
commit 2db86b7829
6 changed files with 56 additions and 76 deletions
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20
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
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@ -270,15 +270,21 @@ class ArgumentDefinition {
* Creates a new argument definition.
* @param source Source information for defining the argument.
*/
public ArgumentDefinition( ArgumentSource source ) {
public ArgumentDefinition( ArgumentSource source,
String fullName,
String shortName,
String doc,
boolean required,
String exclusiveOf,
String validation ) {
this.source = source;
fullName = source.getFullName();
shortName = source.getShortName();
doc = source.getDoc();
required = source.isRequired();
exclusiveOf = source.getExclusiveOf();
validation = source.getValidationRegex();
this.fullName = fullName;
this.shortName = shortName;
this.doc = doc;
this.required = required;
this.exclusiveOf = exclusiveOf;
this.validation = validation;
}
}

65
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentSource.java
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@ -29,6 +29,8 @@ import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.util.Collection;
import java.util.List;
import java.util.Collections;
/**
* Describes the source field which defines a command-line argument.
@ -94,53 +96,26 @@ public class ArgumentSource {
}
/**
* Retrieves the full name of the argument, specifiable with the '--' prefix. The full name can be
* either specified explicitly with the fullName annotation parameter or implied by the field name.
* @return full name of the argument. Never null.
* Generate a list of all argument definitions to which this argument source maps.
* @return A non-null, non-empty list of argument definitions.
*/
public String getFullName() {
return descriptor.fullName().trim().length() > 0 ? descriptor.fullName().trim() : field.getName().toLowerCase();
}
public List<ArgumentDefinition> createArgumentDefinitions() {
String fullName = descriptor.fullName().trim().length() > 0 ? descriptor.fullName().trim() : field.getName().toLowerCase();
String shortName = descriptor.shortName().trim().length() > 0 ? descriptor.shortName().trim() : null;
String doc = descriptor.doc();
boolean required = descriptor.required() && !isFlag();
String exclusiveOf = descriptor.exclusiveOf().trim().length() > 0 ? descriptor.exclusiveOf().trim() : null;
String validation = descriptor.validation().trim().length() > 0 ? descriptor.validation().trim() : null;
/**
* Retrieves the short name of the argument, specifiable with the '-' prefix. The short name can
* be specified or not; if left unspecified, no short name will be present.
* @return short name of the argument. Null if no short name exists.
*/
public String getShortName() {
return descriptor.shortName().trim().length() > 0 ? descriptor.shortName().trim() : null;
}
/**
* Documentation for this argument. Mandatory field.
* @return Documentation for this argument.
*/
public String getDoc() {
return descriptor.doc();
}
/**
* Returns whether this field is required. Note that flag fields are always forced to 'not required'.
* @return True if the field is mandatory and not a boolean flag. False otherwise.
*/
public boolean isRequired() {
return descriptor.required() && !isFlag();
}
/**
* Specifies other arguments which cannot be used in conjunction with tihs argument. Comma-separated list.
* @return A comma-separated list of exclusive arguments, or null if none are present.
*/
public String getExclusiveOf() {
return descriptor.exclusiveOf().trim().length() > 0 ? descriptor.exclusiveOf().trim() : null;
}
/**
* A regular expression which can be used for validation.
* @return a JVM regex-compatible regular expression, or null to permit any possible value.
*/
public String getValidationRegex() {
return descriptor.validation().trim().length() > 0 ? descriptor.validation().trim() : null;
ArgumentDefinition argumentDefinition = new ArgumentDefinition( this,
fullName,
shortName,
doc,
required,
exclusiveOf,
validation );
return Collections.singletonList(argumentDefinition);
}
/**

38
java/src/org/broadinstitute/sting/utils/cmdLine/FieldParser.java → java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
View File

@ -38,54 +38,54 @@ import java.util.*;
* @author mhanna
* @version 0.1
*/
public abstract class FieldParser {
public abstract class ArgumentTypeDescriptor {
/**
* our log, which we want to capture anything from org.broadinstitute.sting
*/
protected static Logger logger = Logger.getLogger(FieldParser.class);
protected static Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class);
/**
* Name of the field which should be parsed by this argument.
*/
protected final String fieldName;
public static FieldParser create( Field field ) {
public static ArgumentTypeDescriptor create( Field field ) {
Class type = field.getType();
if( Collection.class.isAssignableFrom(type) || type.isArray() )
return new JRECompoundFieldParser( field );
return new CompoundArgumentTypeDescriptor( field );
else
return new JRESimpleFieldParser( field );
return new SimpleArgumentTypeDescriptor( field );
}
static FieldParser create( String fieldName, Class type ) {
static ArgumentTypeDescriptor create( String fieldName, Class type ) {
if( Collection.class.isAssignableFrom(type) || type.isArray() )
return new JRECompoundFieldParser( fieldName, type );
return new CompoundArgumentTypeDescriptor( fieldName, type );
else
return new JRESimpleFieldParser( fieldName, type );
return new SimpleArgumentTypeDescriptor( fieldName, type );
}
protected FieldParser( Field field ) {
protected ArgumentTypeDescriptor( Field field ) {
fieldName = field.toString();
}
protected FieldParser( String fieldName ) {
protected ArgumentTypeDescriptor( String fieldName ) {
this.fieldName = fieldName;
}
public abstract Object parse( String... values );
}
class JRESimpleFieldParser extends FieldParser {
class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
private final Class type;
public JRESimpleFieldParser( Field field ) {
public SimpleArgumentTypeDescriptor( Field field ) {
super( field );
this.type = field.getType();
}
public JRESimpleFieldParser( String fieldName, Class type ) {
public SimpleArgumentTypeDescriptor( String fieldName, Class type ) {
super( fieldName );
this.type = type;
}
@ -142,12 +142,12 @@ class JRESimpleFieldParser extends FieldParser {
};
}
class JRECompoundFieldParser extends FieldParser {
class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
private final Class type;
private final Class componentType;
private final FieldParser componentArgumentParser;
private final ArgumentTypeDescriptor componentArgumentParser;
public JRECompoundFieldParser( Field field ) {
public CompoundArgumentTypeDescriptor( Field field ) {
super( field );
Class candidateType = field.getType();
@ -181,10 +181,10 @@ class JRECompoundFieldParser extends FieldParser {
else
throw new StingException("Unsupported compound argument type: " + candidateType);
componentArgumentParser = FieldParser.create( fieldName, componentType );
componentArgumentParser = ArgumentTypeDescriptor.create( fieldName, componentType );
}
public JRECompoundFieldParser( String fieldName, Class type ) {
public CompoundArgumentTypeDescriptor( String fieldName, Class type ) {
super(fieldName);
this.type = type;
@ -198,7 +198,7 @@ class JRECompoundFieldParser extends FieldParser {
else
throw new StingException("Unsupported compound argument type: " + type);
componentArgumentParser = FieldParser.create( fieldName, componentType );
componentArgumentParser = ArgumentTypeDescriptor.create( fieldName, componentType );
}
@Override

6
java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
View File

@ -85,7 +85,7 @@ public class ParsingEngine {
public void addArgumentSource( String sourceName, Class sourceClass ) {
List<ArgumentDefinition> argumentsFromSource = new ArrayList<ArgumentDefinition>();
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass,true) )
argumentsFromSource.add( new ArgumentDefinition(argumentSource) );
argumentsFromSource.addAll( argumentSource.createArgumentDefinitions() );
argumentDefinitions.add( new ArgumentDefinitionGroup(sourceName, argumentsFromSource) );
}
@ -280,7 +280,7 @@ public class ParsingEngine {
if( !definition.source.isFlag() ) {
String[] tokens = match.values().toArray(new String[0]);
FieldParser fieldParser = FieldParser.create(definition.source.field);
ArgumentTypeDescriptor fieldParser = ArgumentTypeDescriptor.create(definition.source.field);
definition.source.setValue( object, fieldParser.parse(tokens) );
}
else
@ -355,7 +355,7 @@ public class ParsingEngine {
* @return Parsed object of the inferred type.
*/
private Object constructFromString(Field f, List<String> strs) {
FieldParser fieldParser = FieldParser.create(f);
ArgumentTypeDescriptor fieldParser = ArgumentTypeDescriptor.create(f);
return fieldParser.parse( strs.toArray(new String[0]) );
}
}

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjectorTest.java → java/test/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjectorTest.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.indels;
package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.OutputTracker;

1
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterTest.java
View File

@ -11,7 +11,6 @@ import org.junit.Test;
import org.junit.Before;
import org.junit.BeforeClass;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.playground.gatk.walkers.indels.CleanedReadInjector;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;