suffic_tree.py: change missmatch to mismatch

src/rmi_splitter/suffix_tree.py

@@ -98,13 +98,13 @@ class Tree:
     General suffixtree
     """
 
-    def __init__(self, missmatch=None):
+    def __init__(self, mismatch=None):
         """
         Initialisation of a General suffixtree
         """
         self.size = 0
         self.root = Node()
-        self.missmatch = missmatch
+        self.mismatch = mismatch
 
     def __del__(self):
         self.root.__del__()
@@ -141,7 +141,7 @@ class Tree:
                 qual=qual,
                 tree=self,
                 cache=cache,
-                missmatch=self.missmatch,
+                mismatch=self.mismatch,
                 verbose=verbose,
             )
             if verbose:
@@ -160,7 +160,7 @@ class TreeCrawler:
     Helper Class to search suffixtree
     """
 
-    def __init__(self, seq, qual, tree, cache=True, missmatch=None,
+    def __init__(self, seq, qual, tree, cache=True, mismatch=None,
                  verbose=False):
         """
         Initialisation of a General suffixtree
@@ -171,7 +171,7 @@ class TreeCrawler:
         self.qual = qual
         self.tree = tree
         self.barcode = None
-        self.missmatch = missmatch
+        self.mismatch = mismatch
         if verbose:
             print(self.seq)
             for i in range(len(self.qual)):
@@ -183,13 +183,13 @@ class TreeCrawler:
 
     def split_search(self, curr_node, pos, dist=0, verbose=False):
         """
-        Multiply the barcode search in case of missmatch
+        Multiply the barcode search in case of mismatch
         """
         if verbose:
             print((pos, self.seq[pos], curr_node.base,
                    list(curr_node.childs.keys()), dist, curr_node.barcode))
         if len(self.seq) > pos+1:
-            # we search with n missmatch
+            # we search with n mismatch
             for base in curr_node.childs.keys():
                 curr_dist = dist
                 search_result = curr_node[base].get_barcode(
@@ -202,9 +202,9 @@ class TreeCrawler:
                     self.barcodes.append(search_result[0])
                 else:
                     # if no results with one missmath we search with n+1
-                    # missmatch
-                    if self.missmatch is not None:
-                        self.missmatch -= 1
+                    # mismatch
+                    if self.mismatch is not None:
+                        self.mismatch -= 1
                     curr_dist += distance(qual=self.qual, pos=pos + 1)
                     self.split_search(
                         curr_node=curr_node[base],
@@ -243,8 +243,8 @@ class TreeCrawler:
             pos=0
         )
         if self.barcode is None:
-            if self.missmatch is not None:
-                self.missmatch -= 1
+            if self.mismatch is not None:
+                self.mismatch -= 1
             dist = distance(qual=self.qual, pos=pos) + pos
             self.split_search(
                 curr_node=curr_node,
@@ -256,8 +256,8 @@ class TreeCrawler:
                 print((self.barcodes, self.dists))
             if self.barcodes:
                 min_dist = max(self.dists)
-                if self.missmatch is not None:
-                    if self.missmatch < 0:
+                if self.mismatch is not None:
+                    if self.mismatch < 0:
                         return None
                 min_dist_index = self.dists.index(min_dist)
                 self.barcode = self.barcodes[min_dist_index]
@@ -272,12 +272,12 @@ class Forest:
     """
     Forest of suffixtree
     """
-    def __init__(self, missmatch=None):
+    def __init__(self, mismatch=None):
         """
         Initialisation of a Forest
         """
         self.adaptators = dict()
-        self.missmatch = missmatch
+        self.mismatch = mismatch
 
     def __del__(self):
         for adaptator in self.adaptators:
@@ -292,7 +292,7 @@ class Forest:
         params: barcode str()
         """
         if adaptator not in self.adaptators:
-            self.adaptators[adaptator] = Tree(missmatch=self.missmatch)
+            self.adaptators[adaptator] = Tree(mismatch=self.mismatch)
         self.adaptators[adaptator].add_sequence(
             sequence=sequence,
             barcode=barcode