add ahoCorasick, hoping to compile on ubuntu

Author: haved

ahoCorasick/ahoc.c

@@ -0,0 +1,86 @@
+
+typedef struct Node {
+  struct Node* parent;
+  struct Node* next[26];
+  char letter;
+  struct Node* longest_suffix;
+  int count;
+} Node;
+
+Node* getNext(Node* node, char letter);
+
+Node* getLongestSuffix(Node* node) {
+  if(node->longest_suffix == 0) {
+    if(node->parent) { //The top node is supposed to have no longest suffix
+      Node* longest = getLongestSuffix(node->parent);
+      if(longest) { //Our parent is not the root node
+        node->longest_suffix = getNext(longest, node->letter);
+      } else { //Our parent is the root node, thus our longest suffix is empty string
+        node->longest_suffix = node->parent;
+      }
+    }
+  }
+  return node->longest_suffix;
+}
+
+Node* getNext(Node* node, char letter) {
+  if(node->next[letter] == 0) {
+    if(node->parent) {
+      //Any not that isn't the root at least has the root as longest suffix
+      Node* longest_suffix = getLongestSuffix(node);
+      node->next[letter] = getNext(longest_suffix, letter);
+    } else {
+      node->next[letter] = node; //We have no suffix because we are root. Ignore this letter
+    }
+  }
+  return node->next[letter];
+}
+
+int getScore(Node* node) {
+  if(node->count < 0) {
+    node->count += 100000;
+    if(node->parent)
+      node->count += getScore(getLongestSuffix(node));
+  }
+  return node->count;
+}
+
+int string_match(char* dna, int dnalen, char* segments, int segment_count, void* data) {
+  int usedNodes = 0;
+  Node* nodes = (Node*) data;
+
+  Node* root = &nodes[usedNodes++];
+
+  for(int i = 0; i < segment_count; i++) {
+    Node* node = root;
+    char c;
+    while((c = *segments)) {
+      c-=65;
+      if(node->next[c] == 0) {
+        Node* newNode = &nodes[usedNodes++];
+        newNode->parent = node;
+        newNode->letter = c;
+        newNode->count = -100000;
+        node->next[c] = newNode;
+      }
+      node = node->next[c];
+      segments++;
+    }
+    node->count++;
+    segments++;
+  }
+
+  int score = 0;
+  Node* node = root;
+  for(int i = 0; i < dnalen; i++) {
+    char c = dna[i]-65;
+    node = getNext(node, c);
+    score += getScore(node);
+  }
+
+  return score;
+}
+
+int main()
+{
+}

ahoCorasick/ahoc.py

@@ -0,0 +1,44 @@
+import ctypes
+import mmap
+import array
+
+libc = ctypes.cdll.LoadLibrary(None)
+mmap_function = libc.mmap
+mmap_function.restype = ctypes.c_void_p
+mmap_function.argtypes = (ctypes.c_void_p, ctypes.c_size_t,
+                          ctypes.c_int, ctypes.c_int,
+                          ctypes.c_int, ctypes.c_size_t)
+CODE_SIZE = 10000
+DATA_SIZE = 100000
+code_address = mmap_function(None, CODE_SIZE,
+                             mmap.PROT_READ | mmap.PROT_WRITE | mmap.PROT_EXEC,
+                             mmap.MAP_PRIVATE | mmap.MAP_ANONYMOUS,
+                             -1, 0)
+if code_address == -1:
+    raise OSError('mmap failed to allocate memory')
+
+import base64
+code=base64.standard_b64decode(b'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')
+assert len(code) <= CODE_SIZE
+ctypes.memmove(code_address, code, len(code))
+
+string_match_type = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p, ctypes.c_int, ctypes.c_char_p, ctypes.c_int, ctypes.c_void_p)
+string_match_c = ctypes.cast(code_address+0x12ac-0x1020, string_match_type)
+
+data = ctypes.create_string_buffer(DATA_SIZE)
+data_address = ctypes.cast(data,ctypes.POINTER(ctypes.c_void_p))
+ctypes.memset(data_address, DATA_SIZE, 0)
+
+def string_match(dna, segments):
+    dna_buf = dna.encode('utf-8')
+    seg_buf = ('\0'.join(segments)+'\0').encode('utf-8')
+
+    dna_len = len(dna_buf)
+    seg_count = len(segments)
+    return string_match_c(dna_buf, dna_len, seg_buf, seg_count, data_address)
+
+highscore = False
+
+dna = "ACTTACTGG"
+segments = ["A", "ACT", "GG"]
+print(string_match(dna, segments))

ahoCorasick/extract.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from subprocess import call
+import base64
+
+call(["gcc", "ahoc.c", "-o", "ahoc.o"])
+call(["objcopy", "--only-section=.text", "-O", "binary", "ahoc.o", "text.o"])
+with open("text.o", "rb") as fil:
+    with open("text.py", "w") as ut:
+        ut.write(f"base64.standard_b64decode({base64.standard_b64encode(fil.read())})")

ahoCorasick/text.py

@@ -0,0 +1 @@
+base64.standard_b64decode(b'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')