From f2fcfe3fc2903de7462c63df8046f107044909b4 Mon Sep 17 00:00:00 2001
From: BenLangmead <langmea@cs.jhu.edu>
Date: Fri, 24 Jul 2015 14:52:00 -0400
Subject: [PATCH] make sure column iterator is j

---
 3.02_GlobalAlignment.ipynb | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/3.02_GlobalAlignment.ipynb b/3.02_GlobalAlignment.ipynb
index fe9c2ee..a400e0a 100644
--- a/3.02_GlobalAlignment.ipynb
+++ b/3.02_GlobalAlignment.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false
    },
@@ -29,7 +29,7 @@
        "0"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
@@ -52,7 +52,7 @@
        "2"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -63,7 +63,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false
    },
@@ -74,7 +74,7 @@
        "4"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -126,8 +126,8 @@
     "        D[i][0] = D[i-1][0] + score[alphabet.index(x[i-1])][-1]\n",
     "\n",
     "    # Initialize first row\n",
-    "    for i in range(1,len(y)+1):\n",
-    "        D[0][i] = D[0][i-1] + score[-1][alphabet.index(y[i-1])]\n",
+    "    for j in range(1,len(y)+1):\n",
+    "        D[0][j] = D[0][j-1] + score[-1][alphabet.index(y[j-1])]\n",
     "        \n",
     "    # Fill rest of the matrix\n",
     "    for i in range(1, len(x)+1):\n",