Fixed recently introduced multiplexer issue where DoC couldn't be written

directly to command-line.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4839 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/ArgumentSource.java

@@ -167,6 +167,23 @@ public class ArgumentSource {
         return field.isAnnotationPresent(Deprecated.class);
     }
 
+    /**
+     * Returns false if a type-specific default can be employed.
+     * @return True to throw in a type specific default.  False otherwise.
+     */
+    public boolean createsTypeDefault() {
+        return typeDescriptor.createsTypeDefault(this);
+    }
+
+    /**
+     * Generates a default for the given type.
+     * @param parsingEngine the parsing engine used to validate this argument type descriptor.
+     * @return A default value for the given type.
+     */
+    public Object createTypeDefault(ParsingEngine parsingEngine) {
+        return typeDescriptor.createTypeDefault(parsingEngine,this,field.getType());
+    }
+
     /**
      * Builds out a new type descriptor for the given dependent argument as a function
      * of the containing object.

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

@@ -84,9 +84,10 @@ public abstract class ArgumentTypeDescriptor {
      * Generates a default for the given type.
      * @param parsingEngine the parsing engine used to validate this argument type descriptor.
      * @param source Source of the command-line argument.
+     * @param type Type of value to create, in case the command-line argument system wants influence.
      * @return A default value for the given type.
      */
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
 
     /**
      * Given the given argument source and attributes, synthesize argument definitions for command-line arguments.
@@ -503,7 +504,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
         if(multiplexer == null || multiplexedIds == null)
             throw new ReviewedStingException("No multiplexed ids available");
 
@@ -514,7 +515,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         for(Object id: multiplexedIds) {
             Object value = null;
             if(componentTypeDescriptor.createsTypeDefault(source))
-                value = componentTypeDescriptor.createTypeDefault(parsingEngine,source);
+                value = componentTypeDescriptor.createTypeDefault(parsingEngine,source,componentType);
             multiplexedMapping.put(id,value);
         }
         return multiplexedMapping;

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

@@ -326,10 +326,8 @@ public class ParsingEngine {
      * @param instance Object into which to inject the value.  The target might be in a container within the instance.
      */
     private void loadValueIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
-        ArgumentTypeDescriptor typeDescriptor = selectBestTypeDescriptor(source.field.getType());
-
         // Nothing to load
-        if( argumentMatches.size() == 0 && !(typeDescriptor.createsTypeDefault(source) && source.isRequired()))
+        if( argumentMatches.size() == 0 && !(source.createsTypeDefault() && source.isRequired()))
             return;
 
         // Target instance into which to inject the value.
@@ -340,7 +338,7 @@ public class ParsingEngine {
             throw new ReviewedStingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
 
         for( Object target: targets ) {
-            Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : typeDescriptor.createTypeDefault(this,source);
+            Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createTypeDefault(this);
 
             JVMUtils.setFieldValue(source.field,target,value);
         }

java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java

@@ -69,12 +69,12 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
         OutputStreamStub stub = new OutputStreamStub(defaultOutputStream);
         engine.addOutput(stub);
-        return createInstanceOfClass(source.field.getType(),stub);        
+        return createInstanceOfClass(type,stub);        
     }
 
     @Override

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -88,7 +88,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
         SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream);

java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java

@@ -108,7 +108,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");        
         VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false, argumentSources, false);