From 93211c1cd8b3f956cc257b5fa1f8aab3c8fe7e8a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 May 2009 18:13:03 +0000
Subject: [PATCH] template for windowmaker utility -- total non-functional

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@625 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../windowmaker/PositionalDataGenerator.java  | 17 ++++
 .../sting/utils/windowmaker/WindowMaker.java  | 85 +++++++++++++++++++
 2 files changed, 102 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/utils/windowmaker/PositionalDataGenerator.java
 create mode 100755 java/src/org/broadinstitute/sting/utils/windowmaker/WindowMaker.java

diff --git a/java/src/org/broadinstitute/sting/utils/windowmaker/PositionalDataGenerator.java b/java/src/org/broadinstitute/sting/utils/windowmaker/PositionalDataGenerator.java
new file mode 100755
index 000000000..37c3e46ae
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/windowmaker/PositionalDataGenerator.java
@@ -0,0 +1,17 @@
+package org.broadinstitute.sting.utils.windowmaker;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Pair;
+
+import java.util.Iterator;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: Apr 14, 2009
+ * Time: 9:33:00 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public interface PositionalDataGenerator<Pos, T> {
+    public Pos lastPos();
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/windowmaker/WindowMaker.java b/java/src/org/broadinstitute/sting/utils/windowmaker/WindowMaker.java
new file mode 100755
index 000000000..a10457dae
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/windowmaker/WindowMaker.java
@@ -0,0 +1,85 @@
+package org.broadinstitute.sting.utils.windowmaker;
+
+import org.broadinstitute.sting.utils.Pair;
+
+import java.util.ArrayList;
+
+/**
+ * System for allowing "windowed" access into a data stream
+ *
+ * User: depristo
+ * Date: May 1, 2009
+ * Time: 3:03:20 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public abstract class WindowMaker<Pos, T> {
+    private PositionalDataGenerator<Pos, T> dataSource;
+
+    public WindowMaker(PositionalDataGenerator pdg)
+    {
+        dataSource = pdg;        
+    }
+
+    /**
+     * 
+     */
+    public abstract boolean hasNext();
+
+    /**
+     * Get the next object in the stream. Does not advance the stream pointer.  Successive peek()
+     * calls return the same object.
+     * 
+     * @return
+     */
+    public abstract Pair<Pos, T> peek();
+
+    /**
+     * Return the next N objects in the stream.  Does not advance the stream pointer.  Successive peek()
+     * calls return the same Array of Objects.
+     *
+     * @param N
+     * @return
+     */
+    public abstract ArrayList<Pair<Pos, T>> peek(int N);
+
+    /**
+     * Pop the leftmost object off the window
+     */
+    public abstract void pop();
+
+    /**
+     * Pop the leftmost N objects off the window
+     * @param N
+     */
+    public abstract void pop(int N);
+
+    /**
+     * Advance the internal stream pointer to from, collect all data until to, and return the data
+     * from -> to as an ArrayList
+     * 
+     * @param from
+     * @param to
+     * @return
+     */
+    public abstract ArrayList<Pair<Pos, T>> speek(Pos from, Pos to);
+
+    /**
+     * Advance the internal stream pointer to from, collect N data units, and return the data
+     * as an ArrayList
+     *
+     * @param from
+     * @param length
+     * @return
+     */
+    public abstract ArrayList<Pair<Pos, T>> speek(Pos from, int N);
+
+
+    /**
+     * Advance the internal stream pointer to from, collect all remaining data units from the
+     * data stream, and return them all as one (potentially large) arraylist
+     *
+     * @param from
+     * @return
+     */
+    public abstract ArrayList<Pair<Pos, T>> speek(Pos from);
+}