RodBinding<T> are properly generic now.

VariantContextRodBinding removed, as RodBinding<VariantContext> is the right style now.

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.commandline;
 
 import org.apache.log4j.Logger;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.Multiplexer;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
@@ -299,10 +300,10 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
         String value = getArgumentValue( defaultDefinition, matches );
         try {
-            // TODO: determine type of internal value via Parameter
-            Constructor ctor = type.getConstructor(Class.class, String.class, String.class, ParsingEngine.class);
-            RodBinding result = (RodBinding)ctor.newInstance(null, source.field.getName(), value, parsingEngine);
             Tags tags = getArgumentTags(matches);
+            Constructor ctor = type.getConstructor(Class.class, String.class, String.class, Tags.class);
+            Class parameterType = getParameterizedTypeClass(source.field.getGenericType());
+            RodBinding result = (RodBinding)ctor.newInstance(parameterType, source.field.getName(), value, tags);
             parsingEngine.addTags(result,tags);
             return result;
         } catch (InvocationTargetException e) {
@@ -315,6 +316,16 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                             value, source.field.getName()));
         }
     }
+
+    private Class getParameterizedTypeClass(Type t) {
+        if ( t instanceof ParameterizedType ) {
+            ParameterizedType parameterizedType = (ParameterizedType)t;
+            if ( parameterizedType.getActualTypeArguments().length != 1 )
+                throw new ReviewedStingException("BUG: more than 1 generic type found on class" + t);
+            return (Class)parameterizedType.getActualTypeArguments()[0];
+        } else
+            throw new ReviewedStingException("BUG: could not find generic type on class " + t);
+    }
 }
 
 /**

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

@@ -27,7 +27,10 @@ package org.broadinstitute.sting.commandline;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.utils.GenomeLoc;
 
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 
 /**
@@ -38,14 +41,14 @@ import java.util.List;
 public class RodBinding<T extends Feature> {
     final String variableName;
     final String source;
-    final ParsingEngine parser;
+    final Tags tags;
     final Class<T> type;
 
-    protected RodBinding(Class<T> type, final String variableName, final String source, final ParsingEngine parser) {
+    public RodBinding(Class<T> type, final String variableName, final String source, final Tags tags) {
         this.type = type;
         this.variableName = variableName;
         this.source = source;
-        this.parser = parser;
+        this.tags = tags;
     }
 
     public String getVariableName() {
@@ -56,16 +59,26 @@ public class RodBinding<T extends Feature> {
         return source;
     }
 
+    // ------------------------------------------------------------------------------------------
+    //
+    //
+    // Accessors should be kept in sync with RefMetaDataTracker
+    //
+    //
+    // ------------------------------------------------------------------------------------------
+
     public List<T> getValues(final RefMetaDataTracker tracker) {
-        return tracker.getValues(variableName, type);
+        return tracker.getValues(type, getVariableName());
+    }
+    public List<T> getValues(final RefMetaDataTracker tracker, final GenomeLoc onlyAtThisLoc) {
+        return tracker.getValues(type, getVariableName(), onlyAtThisLoc);
     }
 
-//    public <T> List<T> getValues(final RefMetaDataTracker tracker, final Class<T> clazz) {
-//        return tracker.getValues(variableName, clazz);
-//    }
-
     public T getFirstValue(final RefMetaDataTracker tracker) {
-        return tracker.getFirstValue(variableName, type);
+        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) {
@@ -77,7 +90,7 @@ public class RodBinding<T extends Feature> {
     }
 
     public Tags getTags() {
-        return parser.getTags(this);
+        return tags;
     }
 
     public String toString() {

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

@@ -1,78 +0,0 @@
-/*
-* Copyright (c) 2011, The Broad Institute
-*
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-*
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-* OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.sting.commandline;
-
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.Collection;
-
-/**
-* A RodBinding representing a walker argument that gets bound to a ROD track containing VariantContexts
-*/
-public class VariantContextRodBinding extends RodBinding {
-    /**
-     * Create a new RodBinding specialized to provide VariantContexts.
-     * @param variableName the name of the field in the walker that we will bind the ROD track too
-     * @param sourceFile the data source from which we will read the VCs
-     * @param parser the Engine parser used to obtain information about this argument, such as its underlying file type
-     */
-    protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
-        super(VariantContext.class, variableName, sourceFile, parser);
-    }
-
-    /**
-     * Forwarding method to identical tracker method
-     */
-    public Collection<VariantContext> getVariantContexts(final RefMetaDataTracker tracker,
-                                                         final GenomeLoc curLocation,
-                                                         final boolean requireStartHere,
-                                                         final boolean takeFirstOnly ) {
-        return tracker.getVariantContexts(variableName, curLocation, requireStartHere, takeFirstOnly);
-    }
-
-    /**
-     * Forwarding method to identical tracker method
-     * @param tracker
-     * @param curLocation
-     * @param requireStartHere
-     * @return
-     */
-    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
-                                            final GenomeLoc curLocation,
-                                            final boolean requireStartHere ) {
-        return tracker.getVariantContext(variableName, curLocation, requireStartHere);
-    }
-
-    /**
-     * Forwarding method to identical tracker method
-     */
-    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
-                                            final GenomeLoc curLocation) {
-        return tracker.getVariantContext(variableName, curLocation);
-    }
-}

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

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -62,10 +63,10 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
     public boolean ALLOW_MISSING_DATA = false;
 
     @Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
-    public VariantContextRodBinding variants;
+    public RodBinding<VariantContext> variants;
 
-    @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
+//    @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
-    public List<RodBinding> variantsList;
+//    public List<RodBinding<Feature>> variantsList;
 
     public void initialize() {
         out.println(Utils.join("\t", fieldsToTake));
@@ -134,11 +135,11 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
         if ( tracker == null ) // RodWalkers can make funky map calls
             return 0;
 
-        for ( RodBinding binding : variantsList )
+//        for ( RodBinding binding : variantsList )
-            System.out.printf("VariantList binding %s tags=%s%n", binding, getToolkit().getTags(binding).getPositionalTags());
+//            System.out.printf("VariantList binding %s tags=%s%n", binding, getToolkit().getTags(binding).getPositionalTags());
 
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
-            VariantContext vc = variants.getVariantContext(tracker, context.getLocation());
+            VariantContext vc = variants.getFirstValue(tracker, context.getLocation());
             if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
                 List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
                 out.println(Utils.join("\t", vals));