{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's make a class that implements an inverted (substring) index where the map data\n",
    "# structure is a sorted list of (substring, offset) pairs.  Query w/ binary search.\n",
    "\n",
    "import sys\n",
    "import bisect # for binary search\n",
    "\n",
    "class IndexSorted(object):\n",
    "    \n",
    "    def __init__(self, t, ln, ival):\n",
    "        \"\"\" Create index, extracting substrings of length 'ln' \"\"\"\n",
    "        self.t = t\n",
    "        self.ln = ln\n",
    "        self.ival = ival\n",
    "        self.index = []\n",
    "        for i in range(len(t)-ln+1):\n",
    "            self.index.append((t[i:i+ln], i)) # add <substr, offset> pair\n",
    "        self.index.sort() # sort pairs\n",
    "    \n",
    "    def query(self, p):\n",
    "        \"\"\" Return candidate alignments for p \"\"\"\n",
    "        st = bisect.bisect_left(self.index, (p[:self.ln], -1)) # binary search\n",
    "        en = bisect.bisect_right(self.index, (p[:self.ln], sys.maxsize)) # binary search\n",
    "        hits = self.index[st:en] # this range of elements corresponds to the hits\n",
    "        return [ h[1] for h in hits ] # return just the offsets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "index = IndexSorted('CGTGCCTACTTACTTACAT', 5, 4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[8, 12]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "index.query('CTTACTTA') # index: give us hints on where to look for this pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "index.query('TTTTTTTT') # index: give us hints on where to look for this pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Now let's make a similar class but using a Python dictionary instead of a sorted\n",
    "# list.  A Python dictionary is basically a hash table.\n",
    "\n",
    "class IndexHash(object):\n",
    "    \n",
    "    def __init__(self, t, ln, ival):\n",
    "        \"\"\" Create index, extracting substrings of length 'ln' \"\"\"\n",
    "        self.t = t\n",
    "        self.ln = ln\n",
    "        self.ival = ival\n",
    "        self.index = {}\n",
    "        for i in range(len(t)-ln+1):\n",
    "            substr = t[i:i+ln]\n",
    "            if substr in self.index:\n",
    "                self.index[substr].append(i) # substring already in dictionary\n",
    "            else:\n",
    "                self.index[substr] = [i] # add to dictionary\n",
    "    \n",
    "    def query(self, p):\n",
    "        \"\"\" Return candidate alignments for p \"\"\"\n",
    "        return self.index.get(p[:self.ln], [])[:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "index2 = IndexHash('CGTGCCTACTTACTTACAT', 5, 4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[8, 12]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "index2.query('CTTACTTA') # index: give us hints on where to look for this pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "index2.query('TTTTTTTT') # index: give us hints on where to look for this pattern "
   ]
  }
 ],
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