Merge remote-tracking branch 'upstream/master'

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)
-
-