From 8fc6a0a68b8073c1ec83e3bf983c18c60d13a016 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 29 Aug 2012 09:25:05 -0400 Subject: [PATCH] Cleanup RefMetaDataTracker before refactoring ReadMetaDataTracker --- .../sting/commandline/RodBinding.java | 9 +++ .../ManagingReferenceOrderedView.java | 2 +- .../datasources/providers/RodLocusView.java | 2 +- .../gatk/refdata/RefMetaDataTracker.java | 69 ++++++++----------- .../ReferenceOrderedViewUnitTest.java | 7 +- .../refdata/RefMetaDataTrackerUnitTest.java | 2 +- 6 files changed, 44 insertions(+), 47 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java index e0b1154c4..15d134fa2 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java +++ b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java @@ -117,6 +117,15 @@ public final class RodBinding { this.bound = true; } + /** + * For testing purposes only. Creates a RodBinding sufficient for looking up associations to rawName + * @param type + * @param rawName + */ + public RodBinding(Class type, final String rawName) { + this(type, rawName, "missing", type.getSimpleName(), new Tags()); + } + /** * Make an unbound RodBinding. Only available for creating the globally unique UNBOUND object * @param type class this unbound RodBinding creates diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java index d065635c8..080ac6686 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java @@ -58,7 +58,7 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView { // todo -- warning, I removed the reference to the name from states bindings.add( state.iterator.seekForward(loc) ); - return new RefMetaDataTracker(bindings, referenceContext); + return new RefMetaDataTracker(bindings); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java index 54f8b44ed..4be7c63c8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java @@ -101,7 +101,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView { public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext referenceContext ) { // special case the interval again -- add it into the ROD if ( interval != null ) { allTracksHere.add(interval); } - return new RefMetaDataTracker(allTracksHere, referenceContext); + return new RefMetaDataTracker(allTracksHere); } public boolean hasNext() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index 2c2ee51bb..7e32ec112 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -5,7 +5,6 @@ import com.google.java.contract.Requires; 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; import org.broadinstitute.sting.utils.GenomeLoc; @@ -32,11 +31,10 @@ import java.util.*; * Time: 3:05:23 PM */ public class RefMetaDataTracker { - // TODO: this should be a list, not a map, actually + // TODO: this should be a list, not a bindings, actually private final static RODRecordList EMPTY_ROD_RECORD_LIST = new RODRecordListImpl("EMPTY"); - final Map map; - final ReferenceContext ref; + final Map bindings; final protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class); // ------------------------------------------------------------------------------------------ @@ -48,28 +46,25 @@ public class RefMetaDataTracker { // ------------------------------------------------------------------------------------------ /** - * Only for testing -- not accesssible in any other context + * Create an tracker with no bindings */ public RefMetaDataTracker() { - ref = null; - map = Collections.emptyMap(); + bindings = Collections.emptyMap(); } - public RefMetaDataTracker(final Collection allBindings, final ReferenceContext ref) { - this.ref = ref; - - // set up the map + public RefMetaDataTracker(final Collection allBindings) { + // set up the bindings if ( allBindings.isEmpty() ) - map = Collections.emptyMap(); + bindings = Collections.emptyMap(); else { - Map tmap = new HashMap(allBindings.size()); + final Map tmap = new HashMap(allBindings.size()); for ( RODRecordList rod : allBindings ) { if ( rod != null && ! rod.isEmpty() ) tmap.put(canonicalName(rod.getName()), rod); } - // ensure that no one modifies the map itself - map = Collections.unmodifiableMap(tmap); + // ensure that no one modifies the bindings itself + bindings = Collections.unmodifiableMap(tmap); } } @@ -99,7 +94,7 @@ public class RefMetaDataTracker { @Requires({"type != null"}) @Ensures("result != null") public List getValues(final Class type) { - return addValues(map.keySet(), type, new ArrayList(), null, false, false); + return addValues(bindings.keySet(), type, new ArrayList(), null, false, false); } /** @@ -114,7 +109,7 @@ public class RefMetaDataTracker { @Requires({"type != null", "onlyAtThisLoc != null"}) @Ensures("result != null") public List getValues(final Class type, final GenomeLoc onlyAtThisLoc) { - return addValues(map.keySet(), type, new ArrayList(), onlyAtThisLoc, true, false); + return addValues(bindings.keySet(), type, new ArrayList(), onlyAtThisLoc, true, false); } /** @@ -296,7 +291,7 @@ public class RefMetaDataTracker { */ @Requires({"rodBinding != null"}) public boolean hasValues(final RodBinding rodBinding) { - return map.containsKey(canonicalName(rodBinding.getName())); + return bindings.containsKey(canonicalName(rodBinding.getName())); } /** @@ -306,7 +301,7 @@ public class RefMetaDataTracker { * @return List of all tracks */ public List getBoundRodTracks() { - return new ArrayList(map.values()); + return new ArrayList(bindings.values()); } /** @@ -314,38 +309,30 @@ public class RefMetaDataTracker { * @return the number of tracks with at least one bound Feature */ public int getNTracksWithBoundFeatures() { - return map.size(); + return bindings.size(); } // ------------------------------------------------------------------------------------------ - // - // - // old style accessors - // - // TODO -- DELETE ME - // - // + // Protected accessors using strings for unit testing // ------------------------------------------------------------------------------------------ - @Deprecated - public boolean hasValues(final String name) { - return map.containsKey(canonicalName(name)); + protected boolean hasValues(final String name) { + return bindings.containsKey(canonicalName(name)); } - @Deprecated - public List getValues(final Class type, final String name) { + protected List getValues(final Class type, final String name) { return addValues(name, type, new ArrayList(), getTrackDataByName(name), null, false, false); } - @Deprecated - public List getValues(final Class type, final String name, final GenomeLoc onlyAtThisLoc) { + + protected List getValues(final Class type, final String name, final GenomeLoc onlyAtThisLoc) { return addValues(name, type, new ArrayList(), getTrackDataByName(name), onlyAtThisLoc, true, false); } - @Deprecated - public T getFirstValue(final Class type, final String name) { + + protected T getFirstValue(final Class type, final String name) { return safeGetFirst(getValues(type, name)); } - @Deprecated - public T getFirstValue(final Class type, final String name, final GenomeLoc onlyAtThisLoc) { + + protected T getFirstValue(final Class type, final String name, final GenomeLoc onlyAtThisLoc) { return safeGetFirst(getValues(type, name, onlyAtThisLoc)); } @@ -366,7 +353,7 @@ public class RefMetaDataTracker { * @return */ @Requires({"l != null"}) - final private T safeGetFirst(final List l) { + private T safeGetFirst(final List l) { return l.isEmpty() ? null : l.get(0); } @@ -435,7 +422,7 @@ public class RefMetaDataTracker { */ private RODRecordList getTrackDataByName(final String name) { final String luName = canonicalName(name); - RODRecordList l = map.get(luName); + RODRecordList l = bindings.get(luName); return l == null ? EMPTY_ROD_RECORD_LIST : l; } @@ -448,7 +435,7 @@ public class RefMetaDataTracker { * @param name the name of the rod * @return canonical name of the rod */ - private final String canonicalName(final String name) { + private String canonicalName(final String name) { // todo -- remove me after switch to RodBinding syntax return name.toLowerCase(); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java index d75beae23..11a7b4cf7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; import org.broad.tribble.Feature; +import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; @@ -89,7 +90,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest { ReferenceOrderedView view = new ManagingReferenceOrderedView( provider ); RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20), null); - TableFeature datum = tracker.getFirstValue(TableFeature.class, "tableTest"); + TableFeature datum = tracker.getFirstValue(new RodBinding(TableFeature.class, "tableTest")); Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect"); Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect"); @@ -115,13 +116,13 @@ public class ReferenceOrderedViewUnitTest extends BaseTest { ReferenceOrderedView view = new ManagingReferenceOrderedView( provider ); RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20), null); - TableFeature datum1 = tracker.getFirstValue(TableFeature.class, "tableTest1"); + TableFeature datum1 = tracker.getFirstValue(new RodBinding(TableFeature.class, "tableTest1")); Assert.assertEquals(datum1.get("COL1"),"C","datum1 parameter for COL1 is incorrect"); Assert.assertEquals(datum1.get("COL2"),"D","datum1 parameter for COL2 is incorrect"); Assert.assertEquals(datum1.get("COL3"),"E","datum1 parameter for COL3 is incorrect"); - TableFeature datum2 = tracker.getFirstValue(TableFeature.class, "tableTest2"); + TableFeature datum2 = tracker.getFirstValue(new RodBinding(TableFeature.class, "tableTest2")); Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect"); Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect"); diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java index 91c18078e..2f73e373c 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java @@ -133,7 +133,7 @@ public class RefMetaDataTrackerUnitTest { List x = new ArrayList(); if ( AValues != null ) x.add(AValues); if ( BValues != null ) x.add(BValues); - return new RefMetaDataTracker(x, context); + return new RefMetaDataTracker(x); } public int nBoundTracks() {