1.1 --- a/allpy/homology.py	Fri Jul 15 17:02:09 2011 +0400
     1.2 +++ b/allpy/homology.py	Fri Jul 15 17:13:01 2011 +0400
     1.3 @@ -444,12 +444,12 @@
     1.4              exit()
     1.5  
     1.6      # MARKUPING
     1.7 -        markups.AlignmentNumberMarkup(alignment)
     1.8 +        alignment.add_markup('number')
     1.9  
    1.10          for sequence in alignment.sequences:
    1.11 -            markups.SequenceNumberMarkup(sequence)
    1.12 +            sequence.add_markup('number')
    1.13              if case and format != "markup":
    1.14 -                markups.SequenceCaseMarkup(sequence)
    1.15 +                sequence.add_markup('case')
    1.16  
    1.17  
    1.18      #letters = ''.join(v[0] for v in seq.markups['case'].as_list())

     2.1 --- a/allpy/structure.py	Fri Jul 15 17:02:09 2011 +0400
     2.2 +++ b/allpy/structure.py	Fri Jul 15 17:13:01 2011 +0400
     2.3 @@ -24,7 +24,6 @@
     2.4  import config
     2.5  from graph import Graph
     2.6  from homology import MonomerHomology
     2.7 -from markups import SequenceNumberMarkup
     2.8  
     2.9  
    2.10  # for pdb-codes
    2.11 @@ -406,11 +405,10 @@
    2.12      def blocks_to_homology(self, file, blocks):
    2.13          """ Apply transitive closure of homology and save as homology classes
    2.14  
    2.15 -        Apply SequenceNumberMarkup to every sequence if it has not been applied
    2.16 +        Add number markup to every sequence if it has not been added
    2.17          """
    2.18          for s in self.sequences:
    2.19 -            if not hasattr(s, SequenceNumberMarkup.name):
    2.20 -                SequenceNumberMarkup(s)
    2.21 +            s.add_markup('number')
    2.22          class_id = 1
    2.23          column2blocks = {}
    2.24          for column in self.columns:

     3.1 --- a/sequence_based_blocks_search/blocks_finder.py	Fri Jul 15 17:02:09 2011 +0400
     3.2 +++ b/sequence_based_blocks_search/blocks_finder.py	Fri Jul 15 17:13:01 2011 +0400
     3.3 @@ -3,7 +3,6 @@
     3.4  import sys
     3.5  sys.path.append("../")
     3.6  from allpy import protein
     3.7 -from allpy.markups import *
     3.8  from allpy.homology import *
     3.9  import copy
    3.10  import math
    3.11 @@ -342,8 +341,7 @@
    3.12      with links created by create_links function"""
    3.13      #creating markup
    3.14      for sequence in alignment.sequences:
    3.15 -        sim=SequenceIndexMarkup(sequence)
    3.16 -        sim.refresh()
    3.17 +        sequence.add_markup('index')
    3.18      #inferring classes_of_equivalence = homologous monomers = connected_components from links
    3.19      output = MonomerHomology()
    3.20      class_number = 0
    3.21 @@ -382,9 +380,8 @@
    3.22          sys.exit()
    3.23      #creating markups
    3.24      for sequence in alignment.sequences:
    3.25 -        sim=SequenceIndexMarkup(sequence)
    3.26 -        sim.refresh()
    3.27 -    aim = AlignmentIndexMarkup(alignment)
    3.28 +        sequence.add_markup('index')
    3.29 +    aim = alignment.add_markup('index')
    3.30      #inferring classes_of_equivalence = homologous monomers = connected_components from links
    3.31      class_number = 0
    3.32      for column in alignment.columns:

     4.1 --- a/utils/extract_pfam.py	Fri Jul 15 17:02:09 2011 +0400
     4.2 +++ b/utils/extract_pfam.py	Fri Jul 15 17:13:01 2011 +0400
     4.3 @@ -103,7 +103,7 @@
     4.4          print seq.name, seq.description
     4.5          print code.pdb_id
     4.6          raise AssertionError()
     4.7 -    markups.SequencePdbResiMarkup(seq).from_pdb()
     4.8 +    seq.add_markup('pdb_resi').from_pdb()
     4.9  
    4.10  def remove_trailing_monomers(seq, columns):
    4.11      for column in columns:
    4.12 @@ -123,17 +123,14 @@
    4.13          # XXX [ This is extremely nasty hack ] XXX
    4.14          # We replace monomer's class with Gap, so that it is written as .
    4.15          # We remove the monomer from the sequence, BUT NOT FROM ALIGNMENT!
    4.16 -        # And we add some junk to monomers (SequenceIndexMarkup),
    4.17 -        # which we keep laying around there, but remove from markups, so
    4.18 -        # that is does not go to file
    4.19          # In the end it works like we want, but
    4.20          # XXX [ KIDS, DON'T TRY TO DO THIS AT HOME! ] XXX
    4.21 -        markups.SequenceIndexMarkup(seq)
    4.22 +        seq.add_markup('index')
    4.23          for monomer in reversed(seq):
    4.24              if not hasattr(monomer, 'pdb_residue'):
    4.25                  monomer.__class__ = Gap
    4.26                  del seq[monomer.index]
    4.27 -        del seq.markups['index']
    4.28 +        seq.remove_markup('index')
    4.29  
    4.30  def clean_aln(aln):
    4.31      aln.sequences = [
    4.32 @@ -160,7 +157,7 @@
    4.33              out_seq = None
    4.34              pdb_codes = parse_pdb_codes(seq)
    4.35              out_seq = append_seq(out_aln, seq, pdb_codes)
    4.36 -            markups.SequenceCaseMarkup(out_seq)
    4.37 +            out_seq.add_markup('case')
    4.38              add_pdb_structure(out_seq, pdb_codes[0])
    4.39          except AssertionError:
    4.40              if out_seq is not None:

     5.1 --- a/utils/rasmol_homology.py	Fri Jul 15 17:02:09 2011 +0400
     5.2 +++ b/utils/rasmol_homology.py	Fri Jul 15 17:13:01 2011 +0400
     5.3 @@ -42,12 +42,12 @@
     5.4  download_pdb = structure.CachedDownloadPdb(cache_dir=options.pdb_cache)
     5.5  
     5.6  alignment = Alignment().append_file(open(options.markup), format='markup')
     5.7 -markups.AlignmentNumberMarkup(alignment)
     5.8 +alignment.add_markup('number')
     5.9  
    5.10  def pdb_loader(sequence):
    5.11      sequence.__class__ = Sequence
    5.12      sequence.markups['pdb_resi'].add_pdb(download_pdb=download_pdb)
    5.13 -    markups.SequenceNumberMarkup(sequence)
    5.14 +    sequence.add_markup('number')
    5.15  
    5.16  hmg = homology.MonomerHomology()
    5.17  hmg.read(options.homology, columns=True)