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

ParsingEngine now maintains the list of rodBindings 

No longer try to reparser objects to find the right fields
Direct support in RodBinding for getTags()
This commit is contained in:
Mark DePristo 2011-07-27 11:36:53 -04:00
parent 9dfb57168a
commit 097828a466
6 changed files with 27 additions and 27 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -299,8 +299,8 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
String value = getArgumentValue( defaultDefinition, matches );
try {
Constructor ctor = type.getConstructor(String.class, String.class);
RodBinding result = (RodBinding)ctor.newInstance(source.field.getName(), value);
Constructor ctor = type.getConstructor(String.class, String.class, ParsingEngine.class);
RodBinding result = (RodBinding)ctor.newInstance(source.field.getName(), value, parsingEngine);
Tags tags = getArgumentTags(matches);
parsingEngine.addTags(result,tags);
return result;

13
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -59,6 +59,11 @@ public class ParsingEngine {
*/
private List<ParsingMethod> parsingMethods = new ArrayList<ParsingMethod>();
/**
* All of the RodBinding objects we've seen while parsing
*/
private List<RodBinding> rodBindings = new ArrayList<RodBinding>();
/**
* Class reference to the different types of descriptors that the create method can create.
* The type of set used must be ordered (but not necessarily sorted).
@ -342,9 +347,16 @@ public class ParsingEngine {
Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createTypeDefault(this);
JVMUtils.setFieldValue(source.field,target,value);
if ( value instanceof RodBinding )
rodBindings.add((RodBinding)value);
}
}
public Collection<RodBinding> getRodBindings() {
return Collections.unmodifiableCollection(rodBindings);
}
/**
* Gets a collection of the container instances of the given type stored within the given target.
* @param source Argument source.
@ -391,7 +403,6 @@ public class ParsingEngine {
return ArgumentTypeDescriptor.selectBest(argumentTypeDescriptors,type);
}
private List<ArgumentSource> extractArgumentSources(Class sourceClass, Field[] parentFields) {
// now simply call into the truly general routine extract argument bindings but with a null
// object so bindings aren't computed

8
public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
View File

@ -34,10 +34,12 @@ import java.util.List;
public class RodBinding {
final String variableName;
final String source;
final ParsingEngine parser;
public RodBinding(final String variableName, final String source) {
protected RodBinding(final String variableName, final String source, final ParsingEngine parser) {
this.variableName = variableName;
this.source = source;
this.parser = parser;
}
public String getVariableName() {
@ -52,6 +54,10 @@ public class RodBinding {
return tracker.getReferenceMetaData(variableName);
}
public Tags getTags() {
return parser.getTags(this);
}
public String toString() {
return String.format("(RodBinding name=%s source=%s)", getVariableName(), getSource());
}

4
public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java
View File

@ -36,8 +36,8 @@ import java.util.List;
*
*/
public class VariantContextRodBinding extends RodBinding {
public VariantContextRodBinding(final String variableName, final String sourceFile) {
super(variableName, sourceFile);
protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
super(variableName, sourceFile, parser);
}
public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {

21
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -25,10 +25,7 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.RodBinding;
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;
@ -100,7 +97,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
loadArgumentsIntoObject(walker);
argumentSources.add(walker);
Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(getRodBindingsInWalker(walker), parser);
Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings, getArgumentCollection().DBSNPFile, parser);
oldStyle.addAll(newStyle);
engine.setReferenceMetaDataFiles(oldStyle);
@ -121,20 +118,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
return 0;
}
private List<RodBinding> getRodBindingsInWalker(Walker<?,?> walker) {
List<RodBinding> rods = new ArrayList<RodBinding>();
for ( ArgumentSource source : parser.extractArgumentSources(walker.getClass()) ) {
Object obj = JVMUtils.getFieldValue(source.field, walker);
if ( obj instanceof RodBinding ) {
System.out.printf("Found rod binding for field %s of %s%n", obj, source.field);
rods.add((RodBinding)obj);
}
}
return rods;
}
/**
* Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
* This report will be written to either STDOUT or to the run repository, depending on the options

4
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
View File

@ -93,7 +93,7 @@ public class ListFileUtils {
* @param RODBindings a text equivale
* @return a list of expanded, bound RODs.
*/
public static Collection<RMDTriplet> unpackRODBindings(final List<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
public static Collection<RMDTriplet> unpackRODBindings(final Collection<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
// todo -- this is a strange home for this code. Move into ROD system
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
@ -141,7 +141,7 @@ public class ListFileUtils {
* @param RODBindings a text equivale
* @return a list of expanded, bound RODs.
*/
public static Collection<RMDTriplet> unpackRODBindings(final List<RodBinding> RODBindings, final ParsingEngine parser) {
public static Collection<RMDTriplet> unpackRODBindings(final Collection<RodBinding> RODBindings, final ParsingEngine parser) {
// todo -- this is a strange home for this code. Move into ROD system
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();