From 7aa654d13f1cf734bb9faa7c9d5053327b61cdb0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 11 Apr 2012 13:49:09 -0400
Subject: [PATCH] New interface for some dev work that Ryan and I are doing;
 only accessible from private walkers right now

---
 .../ActiveRegionBasedAnnotation.java           | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
new file mode 100755
index 000000000..2c1bb0974
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
@@ -0,0 +1,18 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.List;
+import java.util.Map;
+
+// TODO -- make this an abstract class when we move away from InfoFieldAnnotation
+public interface ActiveRegionBasedAnnotation {
+    // return annotations for the given contexts split by sample and then allele
+    public abstract Map<String, Object> annotate(final Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, final VariantContext vc);
+
+    // return the descriptions used for the VCF INFO meta field
+    public abstract List<VCFInfoHeaderLine> getDescriptions();
+}
\ No newline at end of file