I said - delete!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@259 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,122 +0,0 @@
-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;
-}