1 files changed, 177 insertions, 0 deletions
diff --git a/python/src/sa/int_list.pxi b/python/src/sa/int_list.pxi
new file mode 100644
index 00000000..ad14bc9c
--- /dev/null
+++ b/python/src/sa/int_list.pxi
@@ -0,0 +1,177 @@
+# 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 IntList:
+    cdef int size
+    cdef int increment
+    cdef int len
+    cdef int* arr
+
+    def __cinit__(self, int size=0, int increment=1, int initial_len=0):
+        if initial_len > size:
+            size = initial_len
+        self.size = size
+        self.increment = increment
+        self.len = initial_len
+        self.arr = <int*> malloc(size*sizeof(int))
+        memset(self.arr, 0, initial_len*sizeof(int))
+
+    def __str__(self):
+        cdef unsigned i
+        ret = "IntList["
+        for idx in range(self.size):
+            if idx>0:
+                ret += ","
+            ret += str(self.arr[idx])
+        ret += "]"
+        ret += "len="
+        ret += self.len
+        return ret
+
+    def index(self, val):
+        cdef unsigned i
+        for i in range(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 __dealloc__(self):
+        free(self.arr)
+
+    def __getitem__(self, index):
+        cdef int i, j, k
+        if isinstance(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 IntList" % (index, self.len))
+            return self.arr[j]
+        elif isinstance(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 IntList" % (index.start, index.stop, self.len))
+            result = ()
+            for k from i <= k < j:
+                result = result + (self.arr[k],)
+            return result
+        else:
+            raise TypeError("Illegal key type %s for IntList" % 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))
+        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, IntList 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, char* filename):
+        cdef FILE* f
+        f = fopen(filename, "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, char* filename):
+        cdef FILE* f
+        f = fopen(filename, "r")
+        self.read_handle(f)
+        fclose(f)