fixes that make it a bit more consistent with what's shown in the pra…

…ctical, comments make more sense

3.02_GlobalAlignment.ipynb

@@ -2,23 +2,114 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
    "outputs": [],
    "source": [
     "alphabet = ['A', 'C', 'G', 'T']\n",
-    "score = [[0, 4, 2, 4, 8], \\\n",
-    "         [4, 0, 4, 2, 8], \\\n",
-    "         [2, 4, 0, 4, 8], \\\n",
-    "         [4, 2, 4, 0, 8], \\\n",
+    "score = [[0, 4, 2, 4, 8],\n",
+    "         [4, 0, 4, 2, 8],\n",
+    "         [2, 4, 0, 4, 8],\n",
+    "         [4, 2, 4, 0, 8],\n",
     "         [8, 8, 8, 8, 8]]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 9,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# converts from character to its offset in list alphabet\n",
+    "alphabet.index('A')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "2"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "alphabet.index('G')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "4"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# penalty associated with A (from X) mismatching with T (from Y)\n",
+    "score[alphabet.index('A')][alphabet.index('T')]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "8"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# penalty associated with C (from X) being deleted in Y\n",
+    "score[alphabet.index('C')][-1]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -30,28 +121,28 @@
     "    for i in range(len(x)+1):\n",
     "        D.append([0] * (len(y)+1))\n",
     "        \n",
-    "    # Initialize first row and column of matrix\n",
+    "    # Initialize first column\n",
     "    for i in range(1, len(x)+1):\n",
-    "        D[i][0] = D[i-1][0] + score[alphabet.index(x[i-1])][-1]  #!!!!!!!!!\n",
+    "        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",
+    "        D[0][i] = D[0][i-1] + score[-1][alphabet.index(y[i-1])]\n",
     "        \n",
-    "    # Fill in the rest of the matrix\n",
+    "    # Fill rest of the matrix\n",
     "    for i in range(1, len(x)+1):\n",
     "        for j in range(1, len(y)+1):\n",
-    "            distHor = D[i][j-1] + score[4][alphabet.index(y[j-1])]  #!!!!!!!!!\n",
-    "            distVer = D[i-1][j] + score[alphabet.index(x[i-1])][4]  #!!!!!!!\n",
-    "            distDiag = D[i-1][j-1] + score[alphabet.index(x[i-1])][alphabet.index(y[j-1])] #!!\n",
-    "            \n",
+    "            distHor = D[i][j-1] + score[-1][alphabet.index(y[j-1])]\n",
+    "            distVer = D[i-1][j] + score[alphabet.index(x[i-1])][-1]\n",
+    "            distDiag = D[i-1][j-1] + score[alphabet.index(x[i-1])][alphabet.index(y[j-1])]\n",
     "            D[i][j] = min(distHor, distVer, distDiag)\n",
     "    \n",
-    "    # Edit distance is the value in the bottom right corner of the matrix\n",
-    "    return D[-1][-1]"
+    "    return D[-1][-1]  # return value in bottom right corner"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "metadata": {
     "collapsed": false
    },
@@ -73,21 +164,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.4.3"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.10"
   }
  },
  "nbformat": 4,