separate interface for genotypes as opposed to (population) allelic variants

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,140 @@
+package org.broadinstitute.sting.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 Genotype extends Comparable<ReferenceOrderedDatum> {
+    // ----------------------------------------------------------------------
+    //
+    // manipulating the SNP information
+    //
+    // ----------------------------------------------------------------------
+    /** Location of this genotype on the reference (on the forward strand). If the allele is insertion/deletion, the first inserted/deleted base
+     *  is located right <i>after</i> the specified location
+     *
+     * @return position on the genome wrapped in GenomeLoc object
+     */
+    GenomeLoc getLocation();
+
+    /** Returns actual observed alleles on the fwd strand. Allowed to return more than two alleles (@see #getPloidy()). 
+     * @return list of alleles
+     */
+    List<String> getFWDAlleles() ;
+
+    
+    /** Returns bases on the fwd strand in the true reference allele (regardless of whether the reference allele 
+     * was observed at this site in this particular genotype!) 
+     * as a String. String can be empty (if alt allele is insertion into
+     * the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
+     * (if alt is a longer deletion). For the actually observed alleles, see #getFWDAlleles()
+     *
+     * @return reference allele, forward strand
+     */
+    String getFWDRefBases();
+    
+    /** Returns reference base (regardless of whether the reference allele was actually observed. This method 
+     * is similar to getFWDRefBases() except it returns a single char. For non-single letter (non-SNP) variants, behavior
+     * of this method is not specified and can be defined by implementing classes.
+     * @return
+     */
+    char getRef() ;
+
+    /** Is this variant a SNP?
+    *
+    * @return true or false
+    */
+   boolean isSNP();
+
+   /** Returns true if all observed alleles are reference ones. All is<Variant> methods (where Variant=SNP,Insertion, etc) should
+    * return false at a site where isReference() is true to ensure consistency. 
+    * @return
+    */
+   boolean isReference();
+
+   
+   /** 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 phred-scaled confidence for the variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
+   *
+   * @return
+   */
+  double getVariantConfidence();
+
+  /** Returns phred-scaled confidence in called genotype (e.g. MAQ's consensus confidence, or AlleleCaller's
+   * best vs next-best.
+   * @return
+   */
+  double getConsensusConfidence();
+
+
+  /** Returns true if the site has at most two known or observed alleles (ref and non-ref), or false if there are > 2 allelic variants known or observed. When
+   * the implementing class is a genotype, alleles should be always counted including the reference allele whether it was observed in the particular
+   * individual or not: i.e. if the reference is 'C', then both 'CA' and 'AA' genotypes must be reported as bi-allelic, while 'AT' is <i>not</i> bi-allelic (since there are
+   * two allelic variants, 'A' and 'T' <i>in addition</i> to the (known) reference variant 'C'). 
+   * @return
+   */
+  boolean isBiallelic() ;
+
+  /** 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;
+    
+
+
+
+    /** Return actual number of observed alleles (chromosomes) in the genotype.
+     * @return
+     */
+//    int getPloidy() throws IllegalStateException;
+    
+ }