zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

List<RodBinding<T>> now working (sort of). 

At least the argument parsing system tolerates it.
This commit is contained in:
Mark DePristo 2011-07-29 16:11:22 -04:00
parent 6acb4aad3b
commit a6691ab2fd
8 changed files with 67 additions and 53 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

94
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -111,7 +111,7 @@ public abstract class ArgumentTypeDescriptor {
* @return The parsed object.
*/
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, ArgumentMatches matches) {
return parse(parsingEngine, source, source.field.getType(), matches);
return parse(parsingEngine, source, source.field.getGenericType(), matches);
}
/**
@ -133,18 +133,18 @@ public abstract class ArgumentTypeDescriptor {
protected ArgumentDefinition createDefaultArgumentDefinition( ArgumentSource source ) {
Annotation argumentAnnotation = getArgumentAnnotation(source);
return new ArgumentDefinition( ArgumentIOType.getIOType(argumentAnnotation),
source.field.getType(),
ArgumentDefinition.getFullName(argumentAnnotation, source.field.getName()),
ArgumentDefinition.getShortName(argumentAnnotation),
ArgumentDefinition.getDoc(argumentAnnotation),
source.isRequired() && !createsTypeDefault(source) && !source.isFlag() && !source.isDeprecated(),
source.isFlag(),
source.isMultiValued(),
source.isHidden(),
getCollectionComponentType(source.field),
ArgumentDefinition.getExclusiveOf(argumentAnnotation),
ArgumentDefinition.getValidationRegex(argumentAnnotation),
getValidOptions(source) );
source.field.getType(),
ArgumentDefinition.getFullName(argumentAnnotation, source.field.getName()),
ArgumentDefinition.getShortName(argumentAnnotation),
ArgumentDefinition.getDoc(argumentAnnotation),
source.isRequired() && !createsTypeDefault(source) && !source.isFlag() && !source.isDeprecated(),
source.isFlag(),
source.isMultiValued(),
source.isHidden(),
makeRawTypeIfNecessary(getCollectionComponentType(source.field)),
ArgumentDefinition.getExclusiveOf(argumentAnnotation),
ArgumentDefinition.getValidationRegex(argumentAnnotation),
getValidOptions(source) );
}
/**
@ -153,7 +153,7 @@ public abstract class ArgumentTypeDescriptor {
* @return The parameterized component type, or String.class if the parameterized type could not be found.
* @throws IllegalArgumentException If more than one parameterized type is found on the field.
*/
protected Class getCollectionComponentType( Field field ) {
protected Type getCollectionComponentType( Field field ) {
return null;
}
@ -164,7 +164,7 @@ public abstract class ArgumentTypeDescriptor {
* @param matches The argument matches for the argument source, or the individual argument match for a scalar if this is being called to help parse a collection.
* @return The individual parsed object matching the argument match with Class type.
*/
public abstract Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches );
public abstract Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches );
/**
* If the argument source only accepts a small set of options, populate the returned list with
@ -275,6 +275,18 @@ public abstract class ArgumentTypeDescriptor {
public static boolean isArgumentHidden(Field field) {
return field.isAnnotationPresent(Hidden.class);
}
public Class makeRawTypeIfNecessary(Type t) {
if ( t == null )
return null;
else if ( t instanceof ParameterizedType )
return (Class)((ParameterizedType) t).getRawType();
else if ( t instanceof Class ) {
return (Class)t;
} else {
throw new IllegalArgumentException("Unable to determine Class-derived component type of field: " + t);
}
}
}
/**
@ -296,13 +308,13 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
@Override
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches) {
ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
String value = getArgumentValue( defaultDefinition, matches );
try {
Tags tags = getArgumentTags(matches);
Constructor ctor = type.getConstructor(Class.class, String.class, String.class, Tags.class);
Class parameterType = getParameterizedTypeClass(source.field.getGenericType());
Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, Tags.class);
Class parameterType = getParameterizedTypeClass(type);
RodBinding result = (RodBinding)ctor.newInstance(parameterType, source.field.getName(), value, tags);
parsingEngine.addTags(result,tags);
return result;
@ -352,7 +364,8 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
@Override
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Type fulltype, ArgumentMatches matches) {
Class type = makeRawTypeIfNecessary(fulltype);
if (source.isFlag())
return true;
@ -393,7 +406,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
throw e;
} catch (InvocationTargetException e) {
throw new UserException.CommandLineException(String.format("Failed to parse value %s for argument %s. This is most commonly caused by providing an incorrect data type (e.g. a double when an int is required)",
value, source.field.getName()));
value, source.field.getName()));
} catch (Exception e) {
throw new DynamicClassResolutionException(String.class, e);
}
@ -405,7 +418,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
return result;
}
/**
* A mapping of the primitive types to their associated wrapper classes. Is there really no way to infer
@ -436,8 +449,9 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
@Override
@SuppressWarnings("unchecked")
public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Class type, ArgumentMatches matches) {
Class componentType;
public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Type fulltype, ArgumentMatches matches) {
Class type = makeRawTypeIfNecessary(fulltype);
Type componentType;
Object result;
if( Collection.class.isAssignableFrom(type) ) {
@ -452,7 +466,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
componentType = getCollectionComponentType( source.field );
ArgumentTypeDescriptor componentArgumentParser = parsingEngine.selectBestTypeDescriptor(componentType);
ArgumentTypeDescriptor componentArgumentParser = parsingEngine.selectBestTypeDescriptor(makeRawTypeIfNecessary(componentType));
Collection collection;
try {
@ -481,7 +495,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
else if( type.isArray() ) {
componentType = type.getComponentType();
ArgumentTypeDescriptor componentArgumentParser = parsingEngine.selectBestTypeDescriptor(componentType);
ArgumentTypeDescriptor componentArgumentParser = parsingEngine.selectBestTypeDescriptor(makeRawTypeIfNecessary(componentType));
// Assemble a collection of individual values used in this computation.
Collection<ArgumentMatch> values = new ArrayList<ArgumentMatch>();
@ -489,7 +503,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
for( ArgumentMatch value: match )
values.add(value);
result = Array.newInstance(componentType,values.size());
result = Array.newInstance(makeRawTypeIfNecessary(componentType),values.size());
int i = 0;
for( ArgumentMatch value: values ) {
@ -512,16 +526,16 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
* @throws IllegalArgumentException If more than one parameterized type is found on the field.
*/
@Override
protected Class getCollectionComponentType( Field field ) {
// If this is a parameterized collection, find the contained type. If blow up if more than one type exists.
if( field.getGenericType() instanceof ParameterizedType) {
ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();
if( parameterizedType.getActualTypeArguments().length > 1 )
throw new IllegalArgumentException("Unable to determine collection type of field: " + field.toString());
return (Class)parameterizedType.getActualTypeArguments()[0];
}
else
return String.class;
protected Type getCollectionComponentType( Field field ) {
// If this is a parameterized collection, find the contained type. If blow up if more than one type exists.
if( field.getGenericType() instanceof ParameterizedType) {
ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();
if( parameterizedType.getActualTypeArguments().length > 1 )
throw new IllegalArgumentException("Unable to determine collection type of field: " + field.toString());
return parameterizedType.getActualTypeArguments()[0];
}
else
return String.class;
}
}
@ -568,7 +582,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
throw new ReviewedStingException("No multiplexed ids available");
Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
Class componentType = getCollectionComponentType(source.field);
Class componentType = makeRawTypeIfNecessary(getCollectionComponentType(source.field));
ArgumentTypeDescriptor componentTypeDescriptor = parsingEngine.selectBestTypeDescriptor(componentType);
for(Object id: multiplexedIds) {
@ -582,13 +596,13 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
@Override
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches) {
if(multiplexedIds == null)
throw new ReviewedStingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
Class componentType = getCollectionComponentType(source.field);
Class componentType = makeRawTypeIfNecessary(getCollectionComponentType(source.field));
for(Object id: multiplexedIds) {
@ -659,7 +673,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
* @throws IllegalArgumentException If more than one parameterized type is found on the field.
*/
@Override
protected Class getCollectionComponentType( Field field ) {
protected Type getCollectionComponentType( Field field ) {
// Multiplex arguments must resolve to maps from which the clp should extract the second type.
if( field.getGenericType() instanceof ParameterizedType) {
ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();

2
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -30,7 +30,6 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
@ -165,7 +164,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
*/
protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
return Arrays.asList( new VCFWriterArgumentTypeDescriptor(engine,System.out,argumentSources),
new SAMFileReaderArgumentTypeDescriptor(engine),
new SAMFileWriterArgumentTypeDescriptor(engine,System.out),
new OutputStreamArgumentTypeDescriptor(engine,System.out) );
}

5
public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
View File

@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.Type;
/**
* Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.
@ -78,7 +79,7 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
ArgumentDefinition definition = createDefaultArgumentDefinition(source);
String fileName = getArgumentValue( definition, matches );
@ -91,7 +92,7 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
engine.addOutput(stub);
Object result = createInstanceOfClass(type,stub);
Object result = createInstanceOfClass(makeRawTypeIfNecessary(type),stub);
// WARNING: Side effects required by engine!
parsingEngine.addTags(result,getArgumentTags(matches));

3
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
View File

@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import java.io.File;
import java.lang.reflect.Type;
/**
* Describe how to parse SAMFileReaders.
@ -59,7 +60,7 @@ public class SAMFileReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor
}
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
SAMFileReaderBuilder builder = new SAMFileReaderBuilder();
String readerFileName = getArgumentValue( createDefaultArgumentDefinition(source), matches );

3
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.OutputStream;
import java.lang.annotation.Annotation;
import java.lang.reflect.Type;
import java.util.Arrays;
import java.util.List;
@ -102,7 +103,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
}
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
// Extract all possible parameters that could be passed to a BAM file writer?
ArgumentDefinition bamArgumentDefinition = createBAMArgumentDefinition(source);
String writerFileName = getArgumentValue( bamArgumentDefinition, matches );

3
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Type;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
@ -124,7 +125,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
* @return Transform from the matches into the associated argument.
*/
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
ArgumentDefinition defaultArgumentDefinition = createDefaultArgumentDefinition(source);
// Get the filename for the genotype file, if it exists. If not, we'll need to send output to out.
String writerFileName = getArgumentValue(defaultArgumentDefinition,matches);

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
View File

@ -65,8 +65,8 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
public RodBinding<VariantContext> variants;
// @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
// public List<RodBinding<Feature>> variantsList;
@Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
public List<RodBinding<Feature>> variantsList;
public void initialize() {
out.println(Utils.join("\t", fieldsToTake));
@ -135,8 +135,8 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
if ( tracker == null ) // RodWalkers can make funky map calls
return 0;
// for ( RodBinding binding : variantsList )
// System.out.printf("VariantList binding %s tags=%s%n", binding, getToolkit().getTags(binding).getPositionalTags());
for ( RodBinding binding : variantsList )
System.out.printf("VariantList binding %s tags=%s%n", binding, binding.getTags().getPositionalTags());
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
VariantContext vc = variants.getFirstValue(tracker, context.getLocation());

2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -38,7 +38,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
@ -118,7 +117,6 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
List<ArgumentTypeDescriptor> typeDescriptors = new ArrayList<ArgumentTypeDescriptor>();
typeDescriptors.add(new VCFWriterArgumentTypeDescriptor(GATKEngine,System.out,Collections.<Object>emptyList()));
typeDescriptors.add(new SAMFileReaderArgumentTypeDescriptor(GATKEngine));
typeDescriptors.add(new SAMFileWriterArgumentTypeDescriptor(GATKEngine,System.out));
typeDescriptors.add(new OutputStreamArgumentTypeDescriptor(GATKEngine,System.out));
return typeDescriptors;