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RodBinding<T> are properly generic now. 

VariantContextRodBinding removed, as RodBinding<VariantContext> is the right style now.
This commit is contained in:
Mark DePristo 2011-07-29 14:37:12 -04:00
parent 3b799db61a
commit 6acb4aad3b
4 changed files with 44 additions and 97 deletions
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17
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.walkers.Multiplex;
import org.broadinstitute.sting.gatk.walkers.Multiplexer;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
@ -299,10 +300,10 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
String value = getArgumentValue( defaultDefinition, matches );
try {
// TODO: determine type of internal value via Parameter
Constructor ctor = type.getConstructor(Class.class, String.class, String.class, ParsingEngine.class);
RodBinding result = (RodBinding)ctor.newInstance(null, source.field.getName(), value, parsingEngine);
Tags tags = getArgumentTags(matches);
Constructor ctor = type.getConstructor(Class.class, String.class, String.class, Tags.class);
Class parameterType = getParameterizedTypeClass(source.field.getGenericType());
RodBinding result = (RodBinding)ctor.newInstance(parameterType, source.field.getName(), value, tags);
parsingEngine.addTags(result,tags);
return result;
} catch (InvocationTargetException e) {
@ -315,6 +316,16 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
value, source.field.getName()));
}
}
private Class getParameterizedTypeClass(Type t) {
if ( t instanceof ParameterizedType ) {
ParameterizedType parameterizedType = (ParameterizedType)t;
if ( parameterizedType.getActualTypeArguments().length != 1 )
throw new ReviewedStingException("BUG: more than 1 generic type found on class" + t);
return (Class)parameterizedType.getActualTypeArguments()[0];
} else
throw new ReviewedStingException("BUG: could not find generic type on class " + t);
}
}
/**

33
public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
View File

@ -27,7 +27,10 @@ package org.broadinstitute.sting.commandline;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
@ -38,14 +41,14 @@ import java.util.List;
public class RodBinding<T extends Feature> {
final String variableName;
final String source;
final ParsingEngine parser;
final Tags tags;
final Class<T> type;
protected RodBinding(Class<T> type, final String variableName, final String source, final ParsingEngine parser) {
public RodBinding(Class<T> type, final String variableName, final String source, final Tags tags) {
this.type = type;
this.variableName = variableName;
this.source = source;
this.parser = parser;
this.tags = tags;
}
public String getVariableName() {
@ -56,16 +59,26 @@ public class RodBinding<T extends Feature> {
return source;
}
// ------------------------------------------------------------------------------------------
//
//
// Accessors should be kept in sync with RefMetaDataTracker
//
//
// ------------------------------------------------------------------------------------------
public List<T> getValues(final RefMetaDataTracker tracker) {
return tracker.getValues(variableName, type);
return tracker.getValues(type, getVariableName());
}
public List<T> getValues(final RefMetaDataTracker tracker, final GenomeLoc onlyAtThisLoc) {
return tracker.getValues(type, getVariableName(), onlyAtThisLoc);
}
// public <T> List<T> getValues(final RefMetaDataTracker tracker, final Class<T> clazz) {
// return tracker.getValues(variableName, clazz);
// }
public T getFirstValue(final RefMetaDataTracker tracker) {
return tracker.getFirstValue(variableName, type);
return tracker.getFirstValue(type, getVariableName());
}
public T getFirstValue(final RefMetaDataTracker tracker, final GenomeLoc onlyAtThisLoc) {
return tracker.getFirstValue(type, getVariableName(), onlyAtThisLoc);
}
public boolean hasValues(final RefMetaDataTracker tracker) {
@ -77,7 +90,7 @@ public class RodBinding<T extends Feature> {
}
public Tags getTags() {
return parser.getTags(this);
return tags;
}
public String toString() {

78
public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java
View File

@ -1,78 +0,0 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Collection;
/**
* A RodBinding representing a walker argument that gets bound to a ROD track containing VariantContexts
*/
public class VariantContextRodBinding extends RodBinding {
/**
* Create a new RodBinding specialized to provide VariantContexts.
* @param variableName the name of the field in the walker that we will bind the ROD track too
* @param sourceFile the data source from which we will read the VCs
* @param parser the Engine parser used to obtain information about this argument, such as its underlying file type
*/
protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
super(VariantContext.class, variableName, sourceFile, parser);
}
/**
* Forwarding method to identical tracker method
*/
public Collection<VariantContext> getVariantContexts(final RefMetaDataTracker tracker,
final GenomeLoc curLocation,
final boolean requireStartHere,
final boolean takeFirstOnly ) {
return tracker.getVariantContexts(variableName, curLocation, requireStartHere, takeFirstOnly);
}
/**
* Forwarding method to identical tracker method
* @param tracker
* @param curLocation
* @param requireStartHere
* @return
*/
public VariantContext getVariantContext(final RefMetaDataTracker tracker,
final GenomeLoc curLocation,
final boolean requireStartHere ) {
return tracker.getVariantContext(variableName, curLocation, requireStartHere);
}
/**
* Forwarding method to identical tracker method
*/
public VariantContext getVariantContext(final RefMetaDataTracker tracker,
final GenomeLoc curLocation) {
return tracker.getVariantContext(variableName, curLocation);
}
}

13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
View File

@ -24,6 +24,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -62,10 +63,10 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
public boolean ALLOW_MISSING_DATA = false;
@Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
public VariantContextRodBinding variants;
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> 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));
@ -134,11 +135,11 @@ 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, getToolkit().getTags(binding).getPositionalTags());
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
VariantContext vc = variants.getVariantContext(tracker, context.getLocation());
VariantContext vc = variants.getFirstValue(tracker, context.getLocation());
if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
out.println(Utils.join("\t", vals));