merge with upstream

1 files changed, 196 insertions, 0 deletions

diff --git a/sa-extract/cintlist.pyx b/sa-extract/cintlist.pyx
new file mode 100644
index 00000000..9d0a058e
--- /dev/null
+++ b/sa-extract/cintlist.pyx
@@ -0,0 +1,196 @@
+# 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)
+
+