interface representing allele variants/genotype calls

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@256 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/refdata/AllelicVariant.java

@@ -0,0 +1,122 @@
+package org.broadinstitute.sting.playground.gatk.refdata;
+
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Apr 1, 2009
+ * Time: 11:02:03 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public interface AllelicVariant extends Comparable<ReferenceOrderedDatum> {
+    // ----------------------------------------------------------------------
+    //
+    // manipulating the SNP information
+    //
+    // ----------------------------------------------------------------------
+    /** Location of this variant on the reference (on the forward strand).
+     *
+     * @return
+     */
+    GenomeLoc getLocation();
+
+    /** Returns bases in the reference allele as a String. String can be empty (as in insertion into
+     * the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
+     * (for longer indels).
+     *
+     * @return reference allele, forward strand
+     */
+    String getRefBasesFWD();
+
+    /** Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
+     * if variant is not a SNP.
+     *
+     * @return reference base on the forward strand
+     */
+    char getRefSnpFWD() throws IllegalStateException;
+
+    /** Returns bases in the alternative allele as a String. String can be empty (as in deletion from
+     * the reference), can contain a single character (as in SNP or one-base insertion), or multiple characters
+     * (for longer indels).
+     *
+     * @return alternative allele, forward strand
+     */
+    String getAltBasesFWD();
+
+    /** Returns alternative (minor) allele base for a SNP variant as a character; should throw IllegalStateException
+     * if variant is not a SNP.
+     *
+     * @return alternative allele base on the forward starnd
+     */
+    char getAltSnpFWD() throws IllegalStateException;
+
+    /** Is this variant a SNP?
+     *
+     * @return true or false
+     */
+    boolean isSNP();
+
+    /** Is this variant an insertion? The contract requires isIndel() to return true
+     * if this method returns true.
+     *
+     * @return true or false
+     */
+    boolean isInsertion();
+
+    /** Is this variant a deletion? The contract requires isIndel() to return true
+     * if isDeletion() returns true.
+     *
+     * @return true or false
+     */
+    boolean isDeletion();
+
+    /** Is this variant an insertion or a deletion? The contract requires
+     * this to be true if either isInsertion() or isDeletion() returns true. However,
+     * this method is currently allowed to return true even if neither of isInsertion()
+     * and isDeletion() does.
+     * @return
+     */
+    boolean isIndel();
+
+    /** Returns minor allele frequency.
+     *
+     * @return
+     */
+    double getMAF() ;
+
+    /** Is this variant an actual genotype (such as individual call from sequencing, HapMap chip etc), or
+     * population allelic variant (call from pooled sequencing, dbSNP site etc). Only if variant is a genotype, there
+     * is a meaningful question of, e.g., whether it is a het, or homogeneous non-ref.
+     *
+      * @return true if this variant is an actual genotype.
+     */
+    boolean isGenotype();
+
+    /** Returns phred-mapped confidence in variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
+     *
+     * @return
+     */
+    double getVariationConfidence();
+
+    /** Returns phred-mapped confidence in called genotype (e.g. MAQ's consensus confidence, or AlleleCaller's
+     * best vs next-best.
+     * @return
+     */
+    double getConsensusConfidence();
+
+    /** Returns actual observed genotype. Allowed to return more than two alleles (@see #getPloidy()). If this variant
+     * is not a genotype, should throw an IllegalStateException.
+     * @return
+     */
+    List<String> getGenotype() throws IllegalStateException;
+
+    /** Return actual number of observed alleles (chromosomes) in the genotype. If this variant is not a genotype,
+     * should throw IllegalStateException.
+     * @return
+     */
+    int getPloidy() throws IllegalStateException;
+}