1.1 --- a/repeats/repeat_joiner.py	Tue Nov 23 16:26:14 2010 +0300
     1.2 +++ b/repeats/repeat_joiner.py	Tue Nov 23 16:28:20 2010 +0300
     1.3 @@ -33,10 +33,7 @@
     1.4          repeat_joiner._repeats.append(self)
     1.5          self.start = pos_from
     1.6          self.end = pos_to
     1.7 -        # Interval.__init__(self, pos_from, pos_to)
     1.8          self.ori = ori
     1.9 -        self.group_start = None
    1.10 -        self.group_ori = None
    1.11          if chromosome_name not in repeat_joiner:
    1.12              repeat_joiner[chromosome_name] = Chromosome()
    1.13          self.chromosome = repeat_joiner[chromosome_name]
    1.14 @@ -145,48 +142,17 @@
    1.15          self.repeat_groups = []
    1.16          self._repeats = []
    1.17  
    1.18 -    def _treat_repeat(self, used):
    1.19 -        print 'test traverse'
    1.20 -        def treat_repeat(repeat):
    1.21 +    def full_repeats(self):
    1.22 +        used = set()
    1.23 +        for repeat in self._repeats:
    1.24              if repeat not in used:
    1.25 -                print 'traverse00', repeat
    1.26 -                # repeat.group_ori = True
    1.27 +                repeat.group_ori = True
    1.28                  repeat.group_start = repeat.real_start
    1.29                  repeat_group = RepeatGroup()
    1.30                  self.repeat_groups.append(repeat_group)
    1.31                  q = Queue.Queue()
    1.32                  q.put(repeat)
    1.33 -                print q.empty()
    1.34                  while not q.empty():
    1.35 -                    print 'traverse', repeat
    1.36 -                    r = q.get()
    1.37 -                    if r not in used:
    1.38 -                        used.add(r)
    1.39 -                        repeat_group.append(repeat) 
    1.40 -                        for r1 in r.edges():
    1.41 -                            if r1 not in used:
    1.42 -                                q.put(r1)
    1.43 -                                r1.inherit_from(r)
    1.44 -                repeat_group.calc_start()
    1.45 -        return treat_repeat
    1.46 -
    1.47 -
    1.48 -    def full_repeats(self):
    1.49 -        used = set()
    1.50 -        # for chromosome in self.values():
    1.51 -        #    print 'test', chromosome
    1.52 -        for repeat in self._repeats:
    1.53 -            if repeat not in used:
    1.54 -                print 'traverse00', repeat
    1.55 -                # repeat.group_ori = True
    1.56 -                repeat.group_start = repeat.real_start
    1.57 -                repeat_group = RepeatGroup()
    1.58 -                self.repeat_groups.append(repeat_group)
    1.59 -                q = Queue.Queue()
    1.60 -                q.put(repeat)
    1.61 -                print q.empty()
    1.62 -                while not q.empty():
    1.63 -                    print 'traverse', repeat
    1.64                      r = q.get()
    1.65                      if r not in used:
    1.66                          used.add(r)