Indel also implements Interval interface but has its quirks

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@109 348d0f76-0448-11de-a6fe-93d51630548a

playground/java/src/org/broadinstitute/sting/indels/Indel.java

@@ -0,0 +1,155 @@
+package org.broadinstitute.sting.indels;
+
+import org.broadinstitute.sting.utils.Interval;
+
+/**  This class represents an indel as an interval with respect to the <i>original</i> reference and, in addition,
+ * stores the indel type ( (I)nsertion or (D)eletion ) and can return meaningful event size (see below).
+ * Depending on the indel type, the positions on the reference are:
+ *    <ul>
+ *    <li> Deletion ( e.g. deletion of ACAC from the ref: ACGTT[ACAC]TTTAG to ACGTT[]TTTAG) - start and stop of
+ *         the interval are first and last deleted bases on the original reference (those in square brackets in the
+ *         first sequence in the example)
+ *    <li> Insertion ( e.g. insertion of GTGT into the ref: ACGTT{}TTTAG to ACGTT{GTGT}TTTAG) - start is the first
+ *         position on the original reference <i>after</i> the insertion site (after the '}'), and stop is the last
+ *         position <i>before</i> the insertion site (prior to '{').
+ *    </ul>
+ *
+ * Given these definitions, the length of the interval, as returned by getLength() has the meaning of the length of
+ * the event (affected bases) on the original reference: number of deleted bases for deletion and zero for insertion.
+ * The length of the indel itself is returned by getIndelLength(), which is equal to getLength() for deletions and to
+ * the actual number of inserted bases for insertions (while length on the reference, as returned by getLength() is zero).
+ *
+ * The overlaps are also meaningful with the above definitions: if an alignment to (or, in general, an interval on)
+ * the original reference ends prior to <code>start</code>, or starts after <code>stop</code>, it does not overlap
+ * with the indel event (neither spans over deleted region or contains any of the inserted bases).
+ *
+ */
+public class Indel implements Interval {
+
+    public static enum IndelType { I, D };
+	
+	private long mStart;
+    private long mLength;
+    private IndelType mType;
+
+    /** Creates nBases-long indel at specified start position; the object will be unusable
+     * until indel type is set.
+     * @param start start position on the reference
+     * @param nBases number of inserted or deleted bases
+     */
+    //public Indel(long start, long nBases) {
+   //     mType=null;
+   //     mStart=start;
+   //     mLength=nBases;
+   // }
+
+    /** Creates nBases-long indel of the specified type (insertion or deletion), at specified start position.
+     * @param start start position on the reference
+     * @param nBases number of inserted or deleted bases
+     * @param type Indel type: I or D.
+     */
+    public Indel(long start, long nBases, IndelType type) {
+        mType=type;
+        mStart=start;
+        mLength=nBases;
+    }
+
+	/** Start coordinate on the reference; for deletions it is the position of the first deleted base,
+	 * for insertions it is the first base after the insertion.
+	 * This is the "left boundary" of the event on the original reference: every alignment that ends
+     * befor this position on the reference does not overlap with the indel.
+	 * @return indel's left boundary
+	 */
+	public long getStart() { return mStart; }
+
+    /** Sets start position of the interval.
+     *
+     * @param s start coordinate
+     */
+	public void setStart(long s) { mStart = s; }
+
+	/** Indel's stop coordinate on the reference; for deletions it is the position of the last deleted base,
+	 * for insertions it is the last base before the insertion site (which makes it equal to getStart() - 1).
+	 * This is the "right boundary" of the event: every alignment that starts after
+     * this position on the reference
+	 * does not overlap with the indel.
+	 * @return indel's right boundary
+	 */
+	public long getStop() {
+        if ( mType == IndelType.I ) return mStart - 1;
+		else return mStart + mLength - 1;
+	}
+
+    /** This method is not supported in IndelInterval and will throw an exception. Use setIndelLength() instead.
+     *
+     * @param s stop coordinate
+     */
+    public void setStop(long s) {
+        throw new UnsupportedOperationException("Method setStop(long) is not supported in IndelInterval");
+    }
+
+    /** Returns type of this indel ( I or D).
+     *
+     * @return I or D enum element
+     */
+	public IndelType getType() { return mType; }
+
+    /** Sets the number of bases in this indel (i.e. the actual number of inserted or
+     * deleted bases). Stop position will be always correctly computed based on the indel length and indel type.
+     * @param nBases length of the indel (<i>not</i> the length of the event on the original reference!)
+     */
+	public void setIndelLength(long nBases) { mLength = nBases; }
+
+    /** Returns actual number of inserted or deleted bases in the indel.
+     *
+     * @return number of bases (<i>not</i> the event length on the original reference).
+     * @see #getLength()
+     */
+	public long getIndelLength() { return mLength; }
+
+    /**
+     * Returns true if this interval overlaps with i as judjed by getStart() and getStop() positions of the
+     * two interval objects.
+     *
+     * @param i Another interval
+     * @return true iff intervals overlap
+     */
+    @Override
+    public boolean overlapsP(Interval i) {
+        return ! disjointP(i);  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    /**
+     * Returns true if this interval does not overlap with i as judjed by getStart() and getStop() positions of the
+     * two interval objects.
+     *
+     * @param i Another interval
+     * @return true iff intervals do not overlap
+     */
+    @Override
+    public boolean disjointP(Interval i) {
+        return i.getStop() < this.getStart() || i.getStart() > this.getStop();
+    }
+
+    /** Returns length of the region affected by the indel on the original reference. Note that an insertion
+	 *  has length of 0.
+     *  @return length of the event on the original, unmodified reference
+	 */
+    @Override
+	public long getLength() {
+		if ( mType == IndelType.I ) return 0; 
+		return mLength;
+	}
+
+    @Override
+    public boolean equals(Object o) {
+        if ( ! ( o instanceof Indel ) ) return false;
+        Indel i = (Indel)o;
+        return this.mType == i.mType && this.mStart == i.mStart && this.mLength == i.mLength ;
+    }
+
+    @Override
+    public int hashCode() {
+        return (int)( mStart << 2 + mLength );
+    }
+}