Removed from cherry-pick documentation for functions that are not in master

modules/seq/alg/doc/seqalg.rst

@@ -34,66 +34,3 @@
    - Residues in columns where the reference sequence has gaps should not be 
      considered as aligned. There is no information in the pairwise alignment to 
      guide the merging, the result is undefined.
-
-.. autofunction:: AlignToSEQRES
-
-.. autofunction:: AlignmentFromChainView
-
-
-
-.. function:: LocalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
-
-  Performs a Smith/Waterman local alignment of *seq1* and *seq2* and returns
-  the best-scoring alignments as a list of pairwise alignments.
-  
-  **Example:**
-  
-  .. code-block:: python
-  
-    seq_a=seq.CreateSequence('A', 'acdefghiklmn')
-    seq_b=seq.CreateSequence('B', 'acdhiklmn')
-    alns=seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
-    print alns[0].ToString(80)
-    # >>> A acdefghiklmn
-    # >>> B acd---hiklmn
-
-  :param seq1: A valid sequence
-  :type seq1: :class:`~ost.seq.ConstSequenceHandle`
-  :param seq2: A valid sequence  
-  :type seq2: :class:`~ost.seq.ConstSequenceHandle`
-  
-  :param subst_weigth: The substitution weights matrix
-  :type subst_weight: :class:`SubstWeightMatrix`
-  :param gap_open: The gap opening penalty. Must be a negative number
-  :param gap_ext: The gap extension penalty. Must be a negative number
-  :returns: list of best-scoring, non-overlapping alignments of *seq1* and 
-     *seq2*. Since alignments always start with a replacement, the start is
-     stored in the sequence offset of the two sequences.
-
-
-.. function:: GlobalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
-
-  Performs a Needleman/Wunsch global alignment of *seq1* and *seq2* and returns
-  the best-scoring alignment.
-  
-  **Example:**
-  
-  .. code-block:: python
-  
-    seq_a=seq.CreateSequence('A', 'acdefghiklmn')
-    seq_b=seq.CreateSequence('B', 'acdhiklmn')
-    alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
-    print alns[0].ToString(80)
-    # >>> A acdefghiklmn
-    # >>> B acd---hiklmn
-
-  :param seq1: A valid sequence
-  :type seq1: :class:`~ost.seq.ConstSequenceHandle`
-  :param seq2: A valid sequence  
-  :type seq2: :class:`~ost.seq.ConstSequenceHandle`
-  
-  :param subst_weigth: The substitution weights matrix
-  :type subst_weight: :class:`SubstWeightMatrix`
-  :param gap_open: The gap opening penalty. Must be a negative number
-  :param gap_ext: The gap extension penalty. Must be a negative number
-  :returns: best-scoring alignment of *seq1* and *seq2*.