Add Fm index

string_indexing/fm_index.py

@@ -0,0 +1,88 @@
+
+class _FMIndex:
+  def __init__ (self, SA, BWT, text, n):
+    self.L = BWT
+    self.F = '#$' + ''.join(text[SA[i]] for i in range(1, n + 1))
+    self.n = n
+    self.SA = SA
+    self.sample_size = 8 # const for sampling
+
+    #prepare char mapping for F
+    self.mapper_of_chars = { self.F[2] : 0}
+    self.beginnings = [2]
+    last = self.F[2]
+    for i in range(3, n+2):
+      if self.F[i] != last:
+        last = self.F[i]
+        self.beginnings.append(i)
+        self.mapper_of_chars[last] = len(self.beginnings) - 1
+
+    self.len_of_alphabet = len(self.mapper_of_chars)
+
+    #prepare closest samplings
+    current_sample = 0
+    self.closest_sample = [0]
+    for i in range(1, n+2):
+      if abs(current_sample-i) > abs(current_sample + self.sample_size-i) and (i + self.sample_size < self.n):
+        current_sample += self.sample_size
+      self.closest_sample.append(current_sample)
+
+    #Generate values for occ for given samples O(|A|*n)
+    self.occ_in_sample_for_char = { self.L[i]: [0] for i in range(1, n+2)}
+    for c in self.mapper_of_chars:
+      current_value = 0
+      next_sample = self.sample_size
+      for i in range(1, n+2):
+        if self.L[i] == c:
+          current_value += 1
+        if i == next_sample:
+          self.occ_in_sample_for_char[c].append(current_value)
+          next_sample = next_sample + self.sample_size
+
+def from_suffix_array_and_bwt (SA, BWT, text, n):
+  return _FMIndex(SA, BWT, text, n)
+
+# O(|p|)
+def count(fm, p, size):
+  (low, high) = _get_range_of_occurrences(fm, p, size)
+  return max(high - low + 1, 0) if low > -1 else 0
+
+# O(|p| + k) where k is the number or occurances of p in text
+def contains(fm, p, l):
+  (low, high) = _get_range_of_occurrences(fm, p, l)
+  yield from sorted([fm.SA[i-1] for i in range(low, high + 1) if low > -1])
+
+
+def _get_occ(fm, c, i):
+  if fm.closest_sample[i] < i:
+    to_add = sum(1 for c_prim in fm.L[fm.closest_sample[i] + 1:i + 1] if c_prim == c)
+  else:
+    to_add = sum(-1 for c_prim in fm.L[i + 1:fm.closest_sample[i] + 1] if c_prim == c)
+  return fm.occ_in_sample_for_char[c][fm.closest_sample[i] // fm.sample_size] + to_add
+
+def _get_range_of_occurrences(fm, p, size):
+  if size > fm.n or size == 0:
+    return (-1, -1)
+
+  if p[-1] not in fm.mapper_of_chars:
+    return (-1, -1)
+
+  map_idx = fm.mapper_of_chars[p[-1]]
+  l = fm.beginnings[map_idx]
+  r = fm.n + 1
+  if map_idx != fm.len_of_alphabet - 1:
+    r = fm.beginnings[map_idx + 1] - 1
+
+  for i in range(size-1, 0, -1):
+    if p[i] not in fm.mapper_of_chars:
+      return (-1, -1)
+    occurrences_before = _get_occ(fm, p[i], l - 1)
+    occurrences_after = _get_occ(fm, p[i], r)
+    if occurrences_before == occurrences_after:
+      return (-1, -1)
+    map_idx = fm.mapper_of_chars[p[i]]
+    l = fm.beginnings[map_idx] + occurrences_before
+    r = fm.beginnings[map_idx] + occurrences_after - 1
+    if r < l:
+      return (-1, -1)
+  return (l, r)

test/test_exact_string_matching.py

@@ -6,13 +6,20 @@
 
 from generator import rand
 from exact_string_matching import forward, backward, other
-from string_indexing import lcp, suffix_tree, suffix_array
+from string_indexing import lcp, suffix_tree, suffix_array, fm_index
+from compression import burrows_wheeler
 
 def lcp_lr_contains(t, w, n, m):
   SA = suffix_array.skew(t, n)
   LCP_LR = lcp.build_lcp_lr(lcp.kasai(SA, t, n), n)
   return lcp.contains(SA, LCP_LR, t, w, n, m)
 
+def fm_index_contains(t, w, n, m):
+  SA = suffix_array.skew(t, n)
+  BWT = burrows_wheeler.transform_from_suffix_array(SA, t, n)
+  fm = fm_index.from_suffix_array_and_bwt(SA, BWT, t, n)
+  return fm_index.contains(fm, w, m)
+
 EXACT_STRING_MATCHING_ALGORITHMS = [
     [ 'Morris-Pratt', forward.morris_pratt ],
     [ 'Knuth-Morris-Pratt', forward.knuth_morris_pratt ],
@@ -45,6 +52,7 @@ def lcp_lr_contains(t, w, n, m):
             suffix_array.prefix_doubling(t, n), t, w, n, m),
     ],
     [ 'lcp-lr array', lcp_lr_contains ],
+    [ 'Fm index', fm_index_contains]
 ]
 
 class TestExactStringMatching(unittest.TestCase):