1.1 --- a/allpy/structure.py	Sat Mar 26 00:42:07 2011 +0300
     1.2 +++ b/allpy/structure.py	Sat Mar 26 01:09:05 2011 +0300
     1.3 @@ -293,6 +293,15 @@
     1.4               'fasta_dict': json.dumps(js_fasta_dict)}
     1.5          file.write(template.replace('self_js_text', self_js_test))
     1.6  
     1.7 +    def nongap_columns(self):
     1.8 +        """ return list of not pure gap columns """
     1.9 +        self_sequences = set(self.sequences)
    1.10 +        columns = []
    1.11 +        for column in self.columns:
    1.12 +            if set(column.keys()) & self_sequences:
    1.13 +                columns.append(column)
    1.14 +        return columns
    1.15 +
    1.16  class BlockMixin(base.Block, AlignmentMixin):
    1.17      """Mixin to add 3D properties to blocks.
    1.18  
    1.19 @@ -303,13 +312,14 @@
    1.20  
    1.21      def add_surrounded_columns(self, column_set):
    1.22          """ add to column_set non-gap columns surrounded by column_set """
    1.23 -        for i, column in enumerate(self.columns):
    1.24 +        nongap_columns = self.nongap_columns()
    1.25 +        for i, column in enumerate(nongap_columns)
    1.26              if column not in column_set:
    1.27                  if not set(self.sequences) - set(column.keys()): # no gaps
    1.28                      if i > 0\
    1.29 -                    and self.columns[i-1] in column_set\
    1.30 -                    and i < len(self.columns)-1\
    1.31 -                    and self.columns[i+1] in column_set:
    1.32 +                    and nongap_columns[i-1] in column_set\
    1.33 +                    and i < len(nongap_columns)-1\
    1.34 +                    and nongap_columns[i+1] in column_set:
    1.35                          column_set.add(column)
    1.36  
    1.37      def geometrical_cores(self, max_delta=config.delta,