GenotypeMap contains a Map, not extends it

-- On path to replacing it with GenotypeCollection

public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeMap.java

@@ -24,21 +24,46 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import java.util.Collection;
+import java.util.*;
-import java.util.Map;
-import java.util.TreeMap;
 
 /**
  *
  */
-public class GenotypeMap extends TreeMap<String, Genotype> implements Map<String, Genotype> {
+public class GenotypeMap implements Map<String, Genotype> {
+    final TreeMap<String, Genotype> genotypes;
+    boolean immutable = false;
     public final static GenotypeMap NO_GENOTYPES = new GenotypeMap();
 
+    // ---------------------------------------------------------------------------
+    //
+    // private constructors -- you have to use static create methods to make these classes
+    //
+    // ---------------------------------------------------------------------------
+
+    private GenotypeMap() {
+        this(false);
+    }
+
+    private GenotypeMap(boolean immutable) {
+        this(new TreeMap<String, Genotype>(), immutable);
+    }
+
+    private GenotypeMap(final TreeMap<String, Genotype> genotypes, final boolean immutable) {
+        this.genotypes = genotypes;
+        this.immutable = immutable;
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // public static factory methods
+    //
+    // ---------------------------------------------------------------------------
+
     public static final GenotypeMap create() {
         return new GenotypeMap();
     }
 
-    public static final GenotypeMap create(int nGenotypes) {
+    public static final GenotypeMap create(final int nGenotypes) {
         return new GenotypeMap();
     }
 
@@ -46,6 +71,9 @@ public class GenotypeMap extends TreeMap<String, Genotype> implements Map<String
         return create(genotypes.values());
     }
 
+    // todo -- differentiate between empty constructor and copy constructor
+    // todo -- create constructor (Genotype ... genotypes)
+
     public static final GenotypeMap create(final Map<String, Genotype> genotypes) {
         return create(genotypes.values());
     }
@@ -54,13 +82,110 @@ public class GenotypeMap extends TreeMap<String, Genotype> implements Map<String
         if ( genotypes == null )
             return null; // todo -- really should return an empty map
         else {
-            GenotypeMap genotypeMap = new GenotypeMap();
+            GenotypeMap genotypeMap = new GenotypeMap().mutable();
             for ( final Genotype g : genotypes ) {
                 if ( genotypeMap.containsKey(g.getSampleName() ) )
                     throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g);
                 genotypeMap.put(g.getSampleName(), g);
             }
+
+            //return genotypeMap.immutable();  // todo enable when we have time to dive into mutability issue
             return genotypeMap;
         }
     }
+
+    // ---------------------------------------------------------------------------
+    //
+    // Mutability methods
+    //
+    // ---------------------------------------------------------------------------
+
+    public final GenotypeMap mutable() {
+        immutable = false;
+        return this;
+    }
+
+    public final GenotypeMap immutable() {
+        immutable = true;
+        return this;
+    }
+
+    public boolean isMutable() {
+        return ! immutable;
+    }
+
+    public final void checkImmutability() {
+        if ( immutable )
+            throw new IllegalAccessError("GenotypeMap is currently immutable, but a mutator method was invoked on it");
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // Map methods
+    //
+    // ---------------------------------------------------------------------------
+
+    @Override
+    public void clear() {
+        checkImmutability();
+        genotypes.clear();
+    }
+
+    @Override
+    public int size() {
+        return genotypes.size();
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return genotypes.isEmpty();
+    }
+
+    @Override
+    public boolean containsKey(final Object o) {
+        return genotypes.containsKey(o);
+    }
+
+    @Override
+    public boolean containsValue(final Object o) {
+        return genotypes.containsValue(o);
+    }
+
+    @Override
+    public Genotype get(final Object o) {
+        return genotypes.get(o);
+    }
+
+    @Override
+    public Genotype put(final String s, final Genotype genotype) {
+        checkImmutability();
+        return genotypes.put(s, genotype);
+    }
+
+    @Override
+    public Genotype remove(final Object o) {
+        checkImmutability();
+        return genotypes.remove(o);
+    }
+
+    @Override
+    public void putAll(final Map<? extends String, ? extends Genotype> map) {
+        checkImmutability();
+        genotypes.putAll(map);
+    }
+
+    @Override
+    public Set<String> keySet() {
+        return Collections.unmodifiableSet(genotypes.keySet());
+    }
+
+    @Override
+    public Collection<Genotype> values() {
+        return genotypes.values();
+    }
+
+    @Override
+    public Set<Entry<String, Genotype>> entrySet() {
+        return genotypes.entrySet();
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -46,7 +46,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("14f5cdfc6818cbba600cbdf5fe285275"));
+                Arrays.asList("9834f0cef1cd6ba4943a5aaee1ee8be8"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }