a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@794 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/GenotypeList.java

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+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+/** A simple wrapper interface that allows for keeping any of the "main" (point mutation) or "associated" (indel)
+ * genotypes, or both, at any given reference position. This is the abstraction of "complete" genotyping information:
+ * one might have or might have not genotyped independently a base at the given position (point) or an indel right after
+ * that position. The query and getter methods allow clients to figure out what pieces of the genotyping information
+ * are actually available and to retrieve them. Behavior of the getters when corresponding queries return false is
+ * not bound by a contract but it is suggested that they return null or a "trivial" (reference) genotype. 
+ * 
+ * @author asivache
+ *
+ */
+
+public interface GenotypeList {
+	/** Returns true if point mutation genotyping information is available at the
+	 * current position.
+	 * @return
+	 */
+	boolean hasPointGenotype();
+
+	/** Returns true if indel genotyping information is available at the
+	 * current position.
+	 * @return
+	 */
+	boolean hasIndelGenotype();
+	
+	/** Returns point mutation genotyping information if available;
+	 * behavior is not specified in the case when there is no such information.
+	 * @return
+	 */
+	Genotype getPointGenotype();
+
+	/** Returns indel genotyping information if available;
+	 * behavior is not specified in the case when there is no such information.
+	 * @return
+	 */
+	Genotype getIndelGenotype();
+	
+	/** Returns position on the reference the stored genotyping data are associated with. 
+	 * 
+	 * @return
+	 */
+	GenomeLoc getLocation();
+}