InfoFieldAnnotation now an abstract class extended by annotations so doc system works

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -42,7 +42,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class AlleleBalance implements InfoFieldAnnotation {
+public class AlleleBalance extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java

@@ -8,7 +8,7 @@ import java.util.Map;
 
 
 
-public abstract class AnnotationByDepth implements InfoFieldAnnotation {
+public abstract class AnnotationByDepth extends InfoFieldAnnotation {
 
 
     protected int annotationByVariantDepth(final Map<String, Genotype> genotypes, Map<String, AlignmentContext> stratifiedContexts) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java

@@ -46,7 +46,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class BaseCounts implements InfoFieldAnnotation {
+public class BaseCounts extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java

@@ -43,7 +43,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
+public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
     private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation {
+public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 
-public class FisherStrand implements InfoFieldAnnotation, StandardAnnotation {
+public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
     private static final String FS = "FS";
     private static final double MIN_PVALUE = 1E-320;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
+public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         double content = computeGCContent(ref);

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java

@@ -23,7 +23,7 @@ import java.util.Map;
  */
 
 // A set of annotations calculated directly from the GLs
-public class GLstats implements InfoFieldAnnotation, StandardAnnotation {
+public class GLstats extends InfoFieldAnnotation implements StandardAnnotation {
 
     private static final int MIN_SAMPLES = 10;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -48,7 +48,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
-public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
+public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
     private final static boolean DEBUG = false;
     private final static int MIN_CONTEXT_WING_SIZE = 10;
     private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java

@@ -18,7 +18,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation {
+public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgressAnnotation {
 
     private static final int MIN_SAMPLES = 10;
     private static final int MIN_GENOTYPE_QUALITY = 10;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
+public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnotation {
 
     private boolean ANNOTATE_INDELS = true;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java

@@ -19,7 +19,7 @@ import java.util.*;
  * Time: 11:47:33 AM
  * To change this template use File | Settings | File Templates.
  */
-public class IndelType implements InfoFieldAnnotation, ExperimentalAnnotation {
+public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class LowMQ implements InfoFieldAnnotation {
+public class LowMQ extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java

@@ -18,7 +18,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotation {
+public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java

@@ -18,7 +18,7 @@ import java.util.Map;
 
 
 
-public class MappingQualityZeroFraction implements InfoFieldAnnotation, ExperimentalAnnotation {
+public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java

@@ -21,7 +21,7 @@ import java.util.Map;
  * Date: 5/16/11
  */
 
-public class NBaseCount implements InfoFieldAnnotation {
+public class NBaseCount extends InfoFieldAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if( stratifiedContexts.size() == 0 )
             return null;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation {
+public class QualByDepth extends AnnotationByDepth implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java

@@ -20,7 +20,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation {
+public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -21,7 +21,7 @@ import java.util.Map;
 
 
 
-public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnotation {
+public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation {
     static final double INDEL_LIKELIHOOD_THRESH = 0.1;
     static final boolean DEBUG = false;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java

@@ -41,7 +41,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class SampleList implements InfoFieldAnnotation {
+public class SampleList extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( vc.isMonomorphic() || !vc.hasGenotypes() )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class SpanningDeletions implements InfoFieldAnnotation, StandardAnnotation {
+public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java

@@ -24,7 +24,7 @@ import java.util.Map;
  * Time: 3:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class TechnologyComposition implements ExperimentalAnnotation,InfoFieldAnnotation {
+public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation {
     private String nSLX = "NumSLX";
     private String n454 ="Num454";
     private String nSolid = "NumSOLiD";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java

@@ -48,7 +48,7 @@ import java.util.Map.Entry;
  *
  * For details, see:  http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator
  */
-public class GenomicAnnotation implements InfoFieldAnnotation {
+public class GenomicAnnotation extends InfoFieldAnnotation {
 
     public static final String CHR_COLUMN = "chr";
     public static final String START_COLUMN = "start";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java

@@ -4,20 +4,22 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Map;
 
-public interface InfoFieldAnnotation {
+@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator INFO-field annotations", summary = "VariantAnnotator annotations, written to INFO Field")
+public abstract class InfoFieldAnnotation {
 
     // return annotations for the given contexts split by sample
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
+    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
 
     // return the INFO keys
-    public List<String> getKeyNames();
+    public abstract List<String> getKeyNames();
 
     // return the descriptions used for the VCF INFO meta field
-    public List<VCFInfoHeaderLine> getDescriptions();
+    public abstract List<VCFInfoHeaderLine> getDescriptions();
 
 }

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java

@@ -36,7 +36,7 @@ import java.lang.annotation.*;
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.TYPE)
 public @interface DocumentedGATKFeature {
-    public boolean enable() default true;
+    public boolean enable() default false;
     public String groupName();
     public String summary() default "";
     public Class<? extends DocumentedGATKFeatureHandler> handler() default GenericDocumentationHandler.class;

public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java

@@ -57,7 +57,7 @@ public class GATKDoclet {
      * @throws java.io.IOException if output can't be written.
      */
     public static boolean start(RootDoc rootDoc) throws IOException {
-        logger.setLevel(Level.INFO);
+        logger.setLevel(Level.DEBUG);
         // load arguments
         for(String[] options: rootDoc.options()) {
             if(options[0].equals("-build-timestamp"))
@@ -95,6 +95,10 @@ public class GATKDoclet {
         for ( ClassDoc doc : rootDoc.classes() ) {
             logger.debug("Considering " + doc);
             Class clazz = getClassForClassDoc(doc);
+
+            if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance"))
+                logger.debug("foo");
+
             DocumentedGATKFeature feature = getFeatureForClassDoc(doc);
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
             if ( handler != null && handler.shouldBeProcessed(doc) ) {