Cache AGP file and object line counts

ragtag_utilities/AGPFile.py

@@ -73,6 +73,8 @@ def __init__(self, in_file, mode="r"):
         self._comment_lines = []
         self._objects = []
 
+        self._n_lines = 0
+
         # Store info enabling us to keep track of the state of the AGP file
         self._current_obj = None
         self._seen_objs = set()
@@ -106,6 +108,7 @@ def _read_file(self):
                 if line.startswith("#"):
                     if not in_body:
                         self._comment_lines.append(line)
+                        self._n_lines += 1
                     else:
                         raise AGPError(self.fname, line_number, "illegal comment in AGP body")
                     continue
@@ -141,13 +144,15 @@ def _add_line(self, agp_line):
             # Add the new object to our master list
             agp_obj = AGPObject(self.fname, agp_line)
             self._objects.append(agp_obj)
+            self._n_lines += agp_obj.num_lines
 
             # Initialize all the info for this new object
             self._current_obj = agp_obj.obj
             self._seen_objs.add(agp_obj.obj)
 
         else:
             self._objects[-1].add_line(agp_line)
+            self._n_lines += 1
 
     @property
     def agp_version(self):
@@ -160,7 +165,7 @@ def fname(self):
     @property
     def num_lines(self):
         """ Calculate the number of lines in the current state of the AGP file. """
-        return sum([len(self._comment_lines)] + [obj.num_lines for obj in self._objects])
+        return self._n_lines
 
     @property
     def num_objs(self):
@@ -169,13 +174,15 @@ def num_objs(self):
     def add_pragma(self):
         pragma = "## agp-version {}".format(self.agp_version)
         if self._comment_lines:
+            self._n_lines -= len(self._comment_lines)
             new_comment_lines = [pragma]
             for i in self._comment_lines:
                 if i != pragma:
                     new_comment_lines.append(i)
             self._comment_lines = new_comment_lines
         else:
             self._comment_lines.append(pragma)
+        self._n_lines += len(self._comment_lines)
 
     def iterate_objs(self):
         """ Iterate over the objects of the AGP file. """
@@ -197,6 +204,7 @@ def add_comment(self, c):
 
         if c not in self._comment_lines:
             self._comment_lines.append(c)
+            self._n_lines += 1
 
     def add_seq_line(self, obj, obj_beg, obj_end, pid, comp_type, comp, comp_beg, comp_end, orientation):
         """
@@ -244,6 +252,8 @@ def pop_agp_line(self):
         else:
             self._objects[-1].pop_line()
 
+        self._n_lines -= 1
+
     def write(self):
         """ Write the agp contents to a file. """
         with open(self.fname, "w") as f:
@@ -269,6 +279,7 @@ def __init__(self, agp_fname, in_agp_line):
         self.fname = agp_fname
         self._obj = in_agp_line.obj
         self._agp_lines = []
+        self._n_agp_lines = 0
 
         # Store info enabling us to keep track of the state of the object
         self.previous_pid = 0
@@ -300,7 +311,7 @@ def obj_len(self):
 
     @property
     def num_lines(self):
-        return len(self._agp_lines)
+        return self._n_agp_lines
 
     def add_line(self, agp_line):
         # Perform validity checks if this is a new object
@@ -319,6 +330,7 @@ def add_line(self, agp_line):
         self.previous_pid = agp_line.pid
         self.obj_intervals.append((agp_line.obj_beg - 1, agp_line.obj_end))
         self._agp_lines.append(agp_line)
+        self._n_agp_lines += 1
 
     def iterate_lines(self):
         for i in self._agp_lines: