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RefMetaDataTracker now has get() methods accepting RodBindings 

RodBinding no longer duplicates the get() methods in RMDT.  This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
This commit is contained in:
Mark DePristo 2011-07-30 15:34:11 -04:00
parent a6691ab2fd
commit 7b07c4e04e
4 changed files with 87 additions and 54 deletions
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34
public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
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@ -54,41 +54,13 @@ public class RodBinding<T extends Feature> {
public String getVariableName() {
return variableName;
}
public Class<T> getType() {
return type;
}
public String getSource() {
return source;
}
// ------------------------------------------------------------------------------------------
//
//
// Accessors should be kept in sync with RefMetaDataTracker
//
//
// ------------------------------------------------------------------------------------------
public List<T> getValues(final RefMetaDataTracker tracker) {
return tracker.getValues(type, getVariableName());
}
public List<T> getValues(final RefMetaDataTracker tracker, final GenomeLoc onlyAtThisLoc) {
return tracker.getValues(type, getVariableName(), onlyAtThisLoc);
}
public T getFirstValue(final RefMetaDataTracker tracker) {
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) {
return tracker.hasValues(variableName);
}
public List<GATKFeature> getValuesAsGATKFeatures(final RefMetaDataTracker tracker) {
return tracker.getValuesAsGATKFeatures(variableName);
}
public Tags getTags() {
return tags;
}

76
public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
View File

@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.refdata;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
@ -91,45 +93,81 @@ public class RefMetaDataTracker {
//
// ------------------------------------------------------------------------------------------
public <T> List<T> getValues(Class<T> type) {
public <T extends Feature> List<T> getValues(Class<T> type) {
return addValues(map.keySet(), type, new ArrayList<T>(), null, false, false);
}
public <T> List<T> getValues(Class<T> type, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> List<T> getValues(Class<T> type, final GenomeLoc onlyAtThisLoc) {
return addValues(map.keySet(), type, new ArrayList<T>(), onlyAtThisLoc, true, false);
}
public <T> List<T> getValues(Class<T> type, final String name) {
public <T extends Feature> List<T> getValues(Class<T> type, final String name) {
return addValues(name, type, new ArrayList<T>(), getTrackDataByName(name), null, false, false);
}
public <T> List<T> getValues(Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> List<T> getValues(Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
return addValues(name, type, new ArrayList<T>(), getTrackDataByName(name), onlyAtThisLoc, true, false);
}
public <T> List<T> getValues(Class<T> type, final Collection<String> names) {
public <T extends Feature> List<T> getValues(Class<T> type, final Collection<String> names) {
return addValues(names, type, new ArrayList<T>(), null, false, false);
}
public <T> List<T> getValues(Class<T> type, final Collection<String> names, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> List<T> getValues(Class<T> type, final Collection<String> names, final GenomeLoc onlyAtThisLoc) {
return addValues(names, type, new ArrayList<T>(), onlyAtThisLoc, true, false);
}
public <T> T getFirstValue(Class<T> type) {
public <T extends Feature> T getFirstValue(Class<T> type) {
return safeGetFirst(getValues(type));
}
public <T> T getFirstValue(Class<T> type, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> T getFirstValue(Class<T> type, final GenomeLoc onlyAtThisLoc) {
return safeGetFirst(getValues(type, onlyAtThisLoc));
}
public <T> T getFirstValue(Class<T> type, final String name) {
public <T extends Feature> T getFirstValue(Class<T> type, final String name) {
return safeGetFirst(getValues(type, name));
}
public <T> T getFirstValue(Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> T getFirstValue(Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
return safeGetFirst(getValues(type, name, onlyAtThisLoc));
}
public <T> T getFirstValue(Class<T> type, final Collection<String> names) {
public <T extends Feature> T getFirstValue(Class<T> type, final Collection<String> names) {
return safeGetFirst(getValues(type, names));
}
public <T> T getFirstValue(Class<T> type, final Collection<String> names, final GenomeLoc onlyAtThisLoc) {
public <T extends Feature> T getFirstValue(Class<T> type, final Collection<String> names, final GenomeLoc onlyAtThisLoc) {
return safeGetFirst(getValues(type, names, onlyAtThisLoc));
}
final private <T> T safeGetFirst(List<T> l) {
//
// ROD binding accessors
//
public <T extends Feature> List<T> getValues(RodBinding<T> rodBinding) {
return getValues(rodBinding.getType(), rodBinding.getVariableName());
}
public <T extends Feature> List<T> getValues(RodBinding<T> rodBinding, final GenomeLoc onlyAtThisLoc) {
return getValues(rodBinding.getType(), rodBinding.getVariableName(), onlyAtThisLoc);
}
public <T extends Feature> T getFirstValue(RodBinding<T> rodBinding) {
return getFirstValue(rodBinding.getType(), rodBinding.getVariableName());
}
public <T extends Feature> T getFirstValue(RodBinding<T> rodBinding, final GenomeLoc onlyAtThisLoc) {
return getFirstValue(rodBinding.getType(), rodBinding.getVariableName(), onlyAtThisLoc);
}
public boolean hasValues(RodBinding rodBinding) {
return hasValues(rodBinding.getVariableName());
}
public List<GATKFeature> getValuesAsGATKFeatures(RodBinding rodBinding) {
return getValuesAsGATKFeatures(rodBinding.getVariableName());
}
/**
* Helper function for getFirst() operations that takes a list of <T> and
* returns the first element, or null if no such element exists.
*
* TODO: determine specific behavior for l.size() > 1. Do we turn first or an error?
* TODO: right now we return the first. Should be clearer
*
* @param l
* @param <T>
* @return
*/
final private <T extends Feature> T safeGetFirst(List<T> l) {
// todo: should we be warning people here? Throwing an error?
return l.isEmpty() ? null : l.get(0);
}
@ -216,7 +254,7 @@ public class RefMetaDataTracker {
*/
@Deprecated
public List<Object> getValues(final String name) {
return getValues(name, Object.class);
return (List<Object>)(List)getValues(name, Feature.class);
}
/**
@ -229,7 +267,7 @@ public class RefMetaDataTracker {
* Important: The list returned by this function is guaranteed not to be null, but may be empty!
*/
@Deprecated
public <T> List<T> getValues(final String name, final Class<T> clazz) {
public <T extends Feature> List<T> getValues(final String name, final Class<T> clazz) {
RODRecordList list = getTrackDataByName(name);
if (list.isEmpty())
@ -250,11 +288,11 @@ public class RefMetaDataTracker {
*
* @param name the name of the track
* @param clazz the underlying type to return
* @param <T> the type to parameterize on, matching the clazz argument
* @param <T extends Feature> the type to parameterize on, matching the clazz argument
* @return a record of type T, or null if no record is present.
*/
@Deprecated
public <T> T getFirstValue(final String name, final Class<T> clazz) {
public <T extends Feature> T getFirstValue(final String name, final Class<T> clazz) {
RODRecordList objects = getTrackDataByName(name);
if (objects.isEmpty()) return null;
@ -411,7 +449,7 @@ public class RefMetaDataTracker {
addValues("xxx", VariantContext.class, contexts, rodList, curLocation, requireStartHere, takeFirstOnly);
}
private <T> List<T> addValues(final Collection<String> names,
private <T extends Feature> List<T> addValues(final Collection<String> names,
final Class<T> type,
final List<T> values,
final GenomeLoc curLocation,
@ -425,7 +463,7 @@ public class RefMetaDataTracker {
return values;
}
private <T> List<T> addValues(final String name,
private <T extends Feature> List<T> addValues(final String name,
final Class<T> type,
final List<T> values,
final RODRecordList rodList,

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
View File

@ -139,7 +139,7 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
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());
VariantContext vc = tracker.getFirstValue(variants, context.getLocation());
if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
out.println(Utils.join("\t", vals));

29
public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
View File

@ -30,6 +30,8 @@ import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
@ -181,7 +183,7 @@ public class RefMetaDataTrackerUnitTest {
testSimpleBindings("B", tracker, test.BValues);
}
private void testSimpleBindings(String name, RefMetaDataTracker tracker, RODRecordList expected) {
private <T> void testSimpleBindings(String name, RefMetaDataTracker tracker, RODRecordList expected) {
List<Feature> asValues = tracker.getValues(Feature.class, name);
List<GATKFeature> asFeatures = tracker.getValuesAsGATKFeatures(name);
@ -207,8 +209,8 @@ public class RefMetaDataTrackerUnitTest {
}
@Test(enabled = true, dataProvider = "tests")
public void testGetters(MyTest test) {
logger.warn("Testing " + test + " for getFirst() methods");
public void testGettersAsString(MyTest test) {
logger.warn("Testing " + test + " for get() methods");
RefMetaDataTracker tracker = test.makeTracker();
for ( String name : Arrays.asList("A+B", "A", "B") ) {
@ -226,6 +228,27 @@ public class RefMetaDataTrackerUnitTest {
}
}
@Test(enabled = true, dataProvider = "tests")
public void testGettersAsRodBindings(MyTest test) {
logger.warn("Testing " + test + " for get() methods as RodBindings");
RefMetaDataTracker tracker = test.makeTracker();
for ( String nameAsString : Arrays.asList("A", "B") ) {
RodBinding<Feature> binding = new RodBinding(Feature.class, nameAsString, "none", new Tags());
List<Feature> v1 = tracker.getValues(binding);
testGetter(nameAsString, v1, test.expected(nameAsString), true, tracker);
List<Feature> v2 = tracker.getValues(binding, locus);
testGetter(nameAsString, v2, startingHere(test.expected(nameAsString)), true, tracker);
Feature v3 = tracker.getFirstValue(binding);
testGetter(nameAsString, Arrays.asList(v3), test.expected(nameAsString), false, tracker);
Feature v4 = tracker.getFirstValue(binding, locus);
testGetter(nameAsString, Arrays.asList(v4), startingHere(test.expected(nameAsString)), false, tracker);
}
}
private List<GATKFeature> startingHere(List<GATKFeature> l) {
List<GATKFeature> x = new ArrayList<GATKFeature>();
for ( GATKFeature f : l ) if ( f.getStart() == locus.getStart() ) x.add(f);