ParsingEngine now maintains the list of rodBindings

No longer try to reparser objects to find the right fields
Direct support in RodBinding for getTags()

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

@@ -299,8 +299,8 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
         String value = getArgumentValue( defaultDefinition, matches );
         try {
-            Constructor ctor = type.getConstructor(String.class, String.class);
+            Constructor ctor = type.getConstructor(String.class, String.class, ParsingEngine.class);
-            RodBinding result = (RodBinding)ctor.newInstance(source.field.getName(), value);
+            RodBinding result = (RodBinding)ctor.newInstance(source.field.getName(), value, parsingEngine);
             Tags tags = getArgumentTags(matches);
             parsingEngine.addTags(result,tags);
             return result;

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

@@ -59,6 +59,11 @@ public class ParsingEngine {
      */
     private List<ParsingMethod> parsingMethods = new ArrayList<ParsingMethod>();
 
+    /**
+     * All of the RodBinding objects we've seen while parsing
+     */
+    private List<RodBinding> rodBindings = new ArrayList<RodBinding>();
+
     /**
      * Class reference to the different types of descriptors that the create method can create.
      * The type of set used must be ordered (but not necessarily sorted).
@@ -342,9 +347,16 @@ public class ParsingEngine {
             Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createTypeDefault(this);
 
             JVMUtils.setFieldValue(source.field,target,value);
+
+            if ( value instanceof RodBinding )
+                rodBindings.add((RodBinding)value);
         }
     }
 
+    public Collection<RodBinding> getRodBindings() {
+        return Collections.unmodifiableCollection(rodBindings);
+    }
+
     /**
      * Gets a collection of the container instances of the given type stored within the given target.
      * @param source Argument source.
@@ -391,7 +403,6 @@ public class ParsingEngine {
         return ArgumentTypeDescriptor.selectBest(argumentTypeDescriptors,type);
     }
 
-
     private List<ArgumentSource> extractArgumentSources(Class sourceClass, Field[] parentFields) {
         // now simply call into the truly general routine extract argument bindings but with a null
         // object so bindings aren't computed

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

@@ -34,10 +34,12 @@ import java.util.List;
 public class RodBinding {
     final String variableName;
     final String source;
+    final ParsingEngine parser;
 
-    public RodBinding(final String variableName, final String source) {
+    protected RodBinding(final String variableName, final String source, final ParsingEngine parser) {
         this.variableName = variableName;
         this.source = source;
+        this.parser = parser;
     }
 
     public String getVariableName() {
@@ -52,6 +54,10 @@ public class RodBinding {
         return tracker.getReferenceMetaData(variableName);
     }
 
+    public Tags getTags() {
+        return parser.getTags(this);
+    }
+
     public String toString() {
         return String.format("(RodBinding name=%s source=%s)", getVariableName(), getSource());
     }

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

@@ -36,8 +36,8 @@ import java.util.List;
  *
  */
 public class VariantContextRodBinding extends RodBinding {
-    public VariantContextRodBinding(final String variableName, final String sourceFile) {
+    protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
-        super(variableName, sourceFile);
+        super(variableName, sourceFile, parser);
     }
 
     public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {

public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -25,10 +25,7 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.broadinstitute.sting.commandline.ArgumentSource;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
@@ -100,7 +97,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             loadArgumentsIntoObject(walker);
             argumentSources.add(walker);
 
-            Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(getRodBindingsInWalker(walker), parser);
+            Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
             Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings, getArgumentCollection().DBSNPFile, parser);
             oldStyle.addAll(newStyle);
             engine.setReferenceMetaDataFiles(oldStyle);
@@ -121,20 +118,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         return 0;
     }
 
-    private List<RodBinding> getRodBindingsInWalker(Walker<?,?> walker) {
-        List<RodBinding> rods = new ArrayList<RodBinding>();
-
-        for ( ArgumentSource source : parser.extractArgumentSources(walker.getClass()) ) {
-            Object obj = JVMUtils.getFieldValue(source.field, walker);
-            if ( obj instanceof RodBinding ) {
-                System.out.printf("Found rod binding for field %s of %s%n", obj, source.field);
-                rods.add((RodBinding)obj);
-            }
-        }
-
-        return rods;
-    }
-
     /**
      * Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
      * This report will be written to either STDOUT or to the run repository, depending on the options

public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java

@@ -93,7 +93,7 @@ public class ListFileUtils {
      * @param RODBindings a text equivale
      * @return a list of expanded, bound RODs.
      */
-    public static Collection<RMDTriplet> unpackRODBindings(final List<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
+    public static Collection<RMDTriplet> unpackRODBindings(final Collection<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
         // todo -- this is a strange home for this code.  Move into ROD system
         Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
 
@@ -141,7 +141,7 @@ public class ListFileUtils {
      * @param RODBindings a text equivale
      * @return a list of expanded, bound RODs.
      */
-    public static Collection<RMDTriplet> unpackRODBindings(final List<RodBinding> RODBindings, final ParsingEngine parser) {
+    public static Collection<RMDTriplet> unpackRODBindings(final Collection<RodBinding> RODBindings, final ParsingEngine parser) {
         // todo -- this is a strange home for this code.  Move into ROD system
         Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();