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authorChris Dyer <cdyer@cs.cmu.edu>2012-07-27 17:31:00 -0400
committerChris Dyer <cdyer@cs.cmu.edu>2012-07-27 17:31:00 -0400
commitb317e0efd2398d75d70e027bb1e2cf442e683981 (patch)
treeec34aff0ce4e8fb9704d1cd2b7abf00cb9a25b9a /sa-extract/cintlist.pyx
parentb2a8bccb2bd713d9ec081cf3dad0162c2cb492d8 (diff)
remove old suffix array extractor (use the one in python/ instead)
Diffstat (limited to 'sa-extract/cintlist.pyx')
-rw-r--r--sa-extract/cintlist.pyx196
1 files changed, 0 insertions, 196 deletions
diff --git a/sa-extract/cintlist.pyx b/sa-extract/cintlist.pyx
deleted file mode 100644
index 9d0a058e..00000000
--- a/sa-extract/cintlist.pyx
+++ /dev/null
@@ -1,196 +0,0 @@
-# cintlist.pyx
-# defines int arrays in C, with some convenience methods
-# for reading arrays as globs directly from disk.
-# Adam Lopez <alopez@cs.umd.edu>
-
-from libc.stdio cimport FILE, fopen, fread, fwrite, fclose
-from libc.stdlib cimport malloc, realloc, free
-from libc.string cimport memset, memcpy
-
-cdef class CIntList:
-
- def __cinit__(self, size=0, increment=1, initial_len=0):
- if initial_len > size:
- size = initial_len
- self.arr = <int*> malloc(size*sizeof(int))
- memset(self.arr, 0, initial_len*sizeof(int))
-
- def __str__(self):
- ret = "CIntList["
- for idx in xrange(self.size):
- if idx>0:
- ret += ","
- ret += str(self.arr[idx])
- ret += "]"
- ret += "len="
- ret += self.len
- return ret
-
- def index(self, val):
- for i in xrange(self.len):
- if self.arr[i] == val:
- return i
-
- return IndexError
-
- def partition(self,start,end):
- pivot = self.arr[end]
- bottom = start-1
- top = end
- done = 0
- while not done:
- while not done:
- bottom += 1
- if bottom == top:
- done = 1
- break
- if self.arr[bottom] > pivot:
- self.arr[top] = self.arr[bottom]
- break
- while not done:
- top -= 1
- if top == bottom:
- done = 1
- break
- if self.arr[top] < pivot:
- self.arr[bottom] = self.arr[top]
- break
- self.arr[top] = pivot
- return top
-
- def _doquicksort(self,start,end):
- if start < end:
- split = self.partition(start,end)
- self._doquicksort(start,split-1)
- self._doquicksort(split+1,end)
- else:
- return
-
- def sort(self):
- self._doquicksort(0,self.len-1)
-
- def reset(self):
- self.len = 0
-
- def __init__(self, size=0, increment=1, initial_len=0):
- self.size = size
- if initial_len > size:
- self.size = initial_len
- self.increment = increment
- self.len = initial_len
-
-
- def __dealloc__(self):
- free(self.arr)
-
-
- def __getitem__(self, index):
- cdef int i, j, k
-
- if type(index) == int:
- j = index
- if j < 0:
- j = self.len + j
- if j<0 or j>=self.len:
- raise IndexError("Requested index %d of %d-length CIntList" % (index, self.len))
- return self.arr[j]
- elif type(index) == slice:
- i = index.start
- j = index.stop
- if i < 0:
- i = self.len + i
- if j < 0:
- j = self.len + j
- if i < 0 or i >= self.len or j < 0 or j > self.len:
- raise IndexError("Requested index %d:%d of %d-length CIntList" % (index.start, index.stop, self.len))
- result = ()
- for k from i <= k < j:
- result = result + (self.arr[k],)
- return result
- else:
- raise IndexError("Illegal key type %s for CIntList" % (type(index)))
-
- cdef void set(self, int i, int val):
- j = i
- if i<0:
- j = self.len + i
- if j<0 or j>=self.len:
- raise IndexError("Requested index %d of %d-length IntList" % (i, self.len))
- if type(val) != int:
- raise TypeError
- self.arr[j] = val
-
-
- def __setitem__(self, i, val):
- self.set(i, val)
-
- def __len__(self):
- return self.len
-
- def getSize(self):
- return self.size
-
- def append(self, int val):
- self._append(val)
-
- cdef void _append(self, int val):
- if self.len == self.size:
- self.size = self.size + self.increment
- self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
- self.arr[self.len] = val
- self.len = self.len + 1
-
- def extend(self, other):
- self._extend(other)
-
-
- cdef void _extend(self, CIntList other):
- self._extend_arr(other.arr, other.len)
-
-
- cdef void _extend_arr(self, int* other, int other_len):
- if self.size < self.len + other_len:
- self.size = self.len + other_len
- self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
- memcpy(self.arr+self.len, other, other_len*sizeof(int))
- self.len = self.len + other_len
-
-
- cdef void _clear(self):
- free(self.arr)
- self.len = 0
- self.size = 0
- self.arr = <int*> malloc(0)
-
-
- cdef void write_handle(self, FILE* f):
- fwrite(&(self.len), sizeof(int), 1, f)
- fwrite(self.arr, sizeof(int), self.len, f)
-
-
- def write(self, filename):
- cdef FILE* f
- cdef bytes bfilename = filename
- cdef char* cfilename = bfilename
- f = fopen(cfilename, "w")
- self.write_handle(f)
- fclose(f)
-
-
- cdef void read_handle(self, FILE* f):
- (self.arr)
- fread(&(self.len), sizeof(int), 1, f)
- self.arr = <int*> malloc(self.len * sizeof(int))
- self.size = self.len
- fread(self.arr, sizeof(int), self.len, f)
-
-
- def read(self, filename):
- cdef FILE* f
- cdef bytes bfilename = filename
- cdef char* cfilename = bfilename
- f = fopen(cfilename, "r")
- self.read_handle(f)
- fclose(f)
-
-