adding a basic implementation of the Variation interface.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1578 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java

@@ -0,0 +1,109 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaronmckenna
+ * Date: Sep 9, 2009
+ * Time: 9:32:34 PM
+ *
+ * a basic implementation of variant
+ */
+public class BasicVariation implements Variation {
+
+    protected final String mBases;
+    protected final char mRef;
+    protected final int mLength;
+    protected final GenomeLoc mLocation;
+    protected final double mConfidence;
+    /**
+     * the constructor
+     * @param bases the bases that this variant represents
+     * @param reference the reference base
+     * @param length are we a single base variant, or a indel/deletion? length is negitive for an indel,
+     * positive for a indel, and 0 for a substitution
+     */
+    public BasicVariation(String bases, char reference, int length, GenomeLoc location, double confidence) {
+        mBases = bases;
+        mRef = reference;
+        mLength = length;
+        mLocation = location;
+        mConfidence = confidence;
+    }
+
+    @Override
+    public double getNonRefAlleleFrequency() {
+        return -1.0;
+    }
+
+    @Override
+    public VARIANT_TYPE getType() {
+        if (mLength >0) return VARIANT_TYPE.INDEL;
+        if (mLength <0) return VARIANT_TYPE.DELETION;
+        return (isSNP()) ? VARIANT_TYPE.SNP : VARIANT_TYPE.REFERENCE;
+    }
+
+    @Override
+    public boolean isSNP() {
+        if (mLength == 0 && Utils.dupString(mRef,2).equals(mBases)) return true;
+        return false;
+    }
+
+    @Override
+    public boolean isInsertion() {
+        return (mLength > 0);
+    }
+
+    @Override
+    public boolean isDeletion() {
+        return (mLength < 0);
+    }
+
+    @Override
+    public String getBases() {
+        return mBases;
+    }
+
+    @Override
+    public GenomeLoc getLocation() {
+        return mLocation;
+    }
+
+    @Override
+    public String getReference() {
+        return String.valueOf(mRef);
+    }
+
+    @Override
+    public boolean isHet() {
+        if (mLength == 0 && mBases.charAt(0) != mBases.charAt(1)) return true;
+        return false;
+    }
+
+    @Override
+    public boolean isHom() {
+        return !isHet();
+    }
+
+    @Override
+    public double getNegLog10PError() {
+        return mConfidence;
+    }
+
+    @Override
+    public boolean isReference() {
+        if (mLength == 0 && mBases.charAt(0) == mRef && mRef != mBases.charAt(1)) return true;
+        return false;
+    }
+
+    @Override
+    public char getAlternateBase() {
+        if (mLength != 0) {
+            throw new UnsupportedOperationException("Unable to get alternate base for indel / deletion");
+        }
+        if (mBases.charAt(0) == mRef) return mBases.charAt(1);
+        else return mBases.charAt(0);
+    }
+}