From 501e92d4410c82a734172ece60ea55a55fe2e267 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Mar 2009 05:09:56 +0000
Subject: [PATCH] an interface for an interval object and simple minimum
 implementation; note: in contrast to arachne, this is closed interval

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@108 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/Interval.java  | 59 +++++++++++++++
 .../sting/utils/SimpleInterval.java           | 75 +++++++++++++++++++
 2 files changed, 134 insertions(+)
 create mode 100644 playground/java/src/org/broadinstitute/sting/utils/Interval.java
 create mode 100644 playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java

diff --git a/playground/java/src/org/broadinstitute/sting/utils/Interval.java b/playground/java/src/org/broadinstitute/sting/utils/Interval.java
new file mode 100644
index 000000000..b5d2cbe96
--- /dev/null
+++ b/playground/java/src/org/broadinstitute/sting/utils/Interval.java
@@ -0,0 +1,59 @@
+package org.broadinstitute.sting.utils;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Mar 19, 2009
+ * Time: 12:03:39 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+/** Abstraction of a closed interval [start,stop] 
+ *
+ */
+public interface Interval {
+    /** Start position of the interval.
+     *
+     * @return <start> for the interval [start,stop]
+     */
+    public long getStart();
+
+    /** Sets start position of the interval.
+     *
+     * @param s start coordinate
+     */
+    public void setStart(long s);
+
+    /** End position of the interval.
+     *
+     * @return <stop> for the interval [start,stop]
+     */
+    public long getStop();
+
+    /** Sets stop position of the interval.
+     *
+     * @param s stop coordinate
+     */
+    public void setStop(long s);
+
+    /** Length of the interval. There is currently no contract, an implementation may return negative length
+     * or a length inconsistent with getStop() - getStart() + 1 if it chooses so.
+     *
+     * @return a number representing the length of the interval according to specific implementation
+     */
+    public long getLength();
+
+    /** 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
+     */
+    public boolean overlapsP(org.broadinstitute.sting.utils.Interval i);
+
+    /** 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
+     */
+    public boolean disjointP(org.broadinstitute.sting.utils.Interval i);
+}
diff --git a/playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java b/playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java
new file mode 100644
index 000000000..d3a1b0519
--- /dev/null
+++ b/playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java
@@ -0,0 +1,75 @@
+package org.broadinstitute.sting.utils;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Mar 19, 2009
+ * Time: 12:44:37 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+/** Provides minimum complete implementation of Interval interface.
+ */
+public class SimpleInterval implements Interval {
+
+    private long m_start;
+    private long m_stop;
+
+    public SimpleInterval(long start, long stop) { m_start = start; m_stop = stop; }
+
+    public SimpleInterval(Interval i) { m_start = i.getStart(); m_stop = i.getStop(); }
+//    public SimpleInterval() { m_start = -1; m_stop = -2; }
+
+    /** Start position of the interval.
+     *
+     * @return <start> for the interval [start,stop]
+     */
+    @Override
+    public long getStart() { return m_start; }
+
+    /** Sets start position of the interval.
+     *
+     * @param s start coordinate
+     */
+    public void setStart(long s) { m_start = s; }
+
+    /** End position of the interval.
+     *
+     * @return <stop> for the interval [start,stop]
+     */
+    @Override
+    public long getStop() { return m_stop; }
+
+    /** Sets stop position of the interval.
+     *
+     * @param s stop coordinate
+     */
+    public void setStop(long s) { m_stop = s; }
+
+    /** Length of the interval. This default implementation returns getStop() - getStart() + 1.
+     *
+     * @return
+     */
+    @Override
+    public long getLength() { return (m_stop - m_start + 1); };
+
+    /** 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(org.broadinstitute.sting.utils.Interval i) {
+        return ! disjointP(i);
+    }
+
+    /** 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(org.broadinstitute.sting.utils.Interval i) {
+        return ( i.getStop() < this.m_start || i.getStart() > this.m_stop );
+    }
+}