Cleanup RefMetaDataTracker before refactoring ReadMetaDataTracker

public/java/src/org/broadinstitute/sting/commandline/RodBinding.java

@@ -117,6 +117,15 @@ public final class RodBinding<T extends Feature> {
         this.bound = true;
     }
 
+    /**
+     * For testing purposes only.  Creates a RodBinding sufficient for looking up associations to rawName
+     * @param type
+     * @param rawName
+     */
+    public RodBinding(Class<T> type, final String rawName) {
+        this(type, rawName, "missing", type.getSimpleName(), new Tags());
+    }
+
     /**
      * Make an unbound RodBinding<T>.  Only available for creating the globally unique UNBOUND object
      * @param type class this unbound RodBinding creates

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);
     }
 
     /**

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() {

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<String, RODRecordList> map;
+    final Map<String, RODRecordList> bindings;
-    final ReferenceContext ref;
     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;
+        bindings = Collections.emptyMap();
-        map = Collections.emptyMap();
     }
 
-    public RefMetaDataTracker(final Collection<RODRecordList> allBindings, final ReferenceContext ref) {
+    public RefMetaDataTracker(final Collection<RODRecordList> allBindings) {
-        this.ref = ref;
+        // set up the bindings
-
-        // set up the map
         if ( allBindings.isEmpty() )
-            map = Collections.emptyMap();
+            bindings = Collections.emptyMap();
         else {
-            Map<String, RODRecordList> tmap = new HashMap<String, RODRecordList>(allBindings.size());
+            final Map<String, RODRecordList> tmap = new HashMap<String, RODRecordList>(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
+            // ensure that no one modifies the bindings itself
-            map = Collections.unmodifiableMap(tmap);
+            bindings = Collections.unmodifiableMap(tmap);
         }
     }
 
@@ -99,7 +94,7 @@ public class RefMetaDataTracker {
     @Requires({"type != null"})
     @Ensures("result != null")
     public <T extends Feature> List<T> getValues(final Class<T> type) {
-        return addValues(map.keySet(), type, new ArrayList<T>(), null, false, false);
+        return addValues(bindings.keySet(), type, new ArrayList<T>(), null, false, false);
     }
 
     /**
@@ -114,7 +109,7 @@ public class RefMetaDataTracker {
     @Requires({"type != null", "onlyAtThisLoc != null"})
     @Ensures("result != null")
     public <T extends Feature> List<T> getValues(final Class<T> type, final GenomeLoc onlyAtThisLoc) {
-        return addValues(map.keySet(), type, new ArrayList<T>(), onlyAtThisLoc, true, false);
+        return addValues(bindings.keySet(), type, new ArrayList<T>(), 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<RODRecordList> getBoundRodTracks() {
-        return new ArrayList<RODRecordList>(map.values());
+        return new ArrayList<RODRecordList>(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();
     }
 
     // ------------------------------------------------------------------------------------------
-    //
+    // Protected accessors using strings for unit testing
-    //
-    // old style accessors
-    //
-    // TODO -- DELETE ME
-    //
-    //
     // ------------------------------------------------------------------------------------------
 
-    @Deprecated
+    protected boolean hasValues(final String name) {
-    public boolean hasValues(final String name) {
+        return bindings.containsKey(canonicalName(name));
-        return map.containsKey(canonicalName(name));
     }
 
-    @Deprecated
+    protected <T extends Feature> List<T> getValues(final Class<T> type, final String name) {
-    public <T extends Feature> List<T> getValues(final Class<T> type, final String name) {
         return addValues(name, type, new ArrayList<T>(), getTrackDataByName(name), null, false, false);
     }
-    @Deprecated
+
-    public <T extends Feature> List<T> getValues(final Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
+    protected <T extends Feature> List<T> getValues(final Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
         return addValues(name, type, new ArrayList<T>(), getTrackDataByName(name), onlyAtThisLoc, true, false);
     }
-    @Deprecated
+
-    public <T extends Feature> T getFirstValue(final Class<T> type, final String name) {
+    protected <T extends Feature> T getFirstValue(final Class<T> type, final String name) {
         return safeGetFirst(getValues(type, name));
     }
-    @Deprecated
+
-    public <T extends Feature> T getFirstValue(final Class<T> type, final String name, final GenomeLoc onlyAtThisLoc) {
+    protected <T extends Feature> T getFirstValue(final Class<T> 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 extends Feature> T safeGetFirst(final List<T> l) {
+    private <T extends Feature> T safeGetFirst(final List<T> 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();
     }

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>(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>(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>(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");

public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java

@@ -133,7 +133,7 @@ public class RefMetaDataTrackerUnitTest {
             List<RODRecordList> x = new ArrayList<RODRecordList>();
             if ( AValues != null ) x.add(AValues);
             if ( BValues != null ) x.add(BValues);
-            return new RefMetaDataTracker(x, context);
+            return new RefMetaDataTracker(x);
         }
 
         public int nBoundTracks() {