bio-alignment 0.0.5 → 0.0.6
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- data/Gemfile +5 -4
- data/README.md +94 -9
- data/Rakefile +2 -1
- data/VERSION +1 -1
- data/doc/bio-alignment-design.md +75 -11
- data/features/bioruby-feature.rb +17 -0
- data/features/bioruby.feature +6 -1
- data/features/columns-feature.rb +2 -0
- data/features/edit/del_bridges-feature.rb +7 -3
- data/features/edit/del_bridges.feature +1 -2
- data/features/edit/del_non_informative_sequences-feature.rb +26 -0
- data/features/edit/del_non_informative_sequences.feature +19 -0
- data/features/edit/del_short_sequences-feature.rb +21 -0
- data/features/edit/del_short_sequences.feature +25 -0
- data/features/edit/gblocks-feature.rb +2 -2
- data/features/edit/mask_islands-feature.rb +17 -4
- data/features/edit/mask_islands.feature +28 -17
- data/features/edit/mask_serial_mutations-feature.rb +8 -6
- data/features/edit/mask_serial_mutations.feature +11 -11
- data/features/tree-feature.rb +66 -0
- data/features/tree.feature +45 -0
- data/lib/bio-alignment.rb +4 -1
- data/lib/bio-alignment/alignment.rb +58 -3
- data/lib/bio-alignment/codonsequence.rb +14 -2
- data/lib/bio-alignment/columns.rb +102 -0
- data/lib/bio-alignment/edit/del_bridges.rb +18 -1
- data/lib/bio-alignment/edit/del_non_informative_sequences.rb +27 -0
- data/lib/bio-alignment/edit/del_short_sequences.rb +28 -0
- data/lib/bio-alignment/edit/edit_columns.rb +22 -0
- data/lib/bio-alignment/edit/edit_rows.rb +49 -0
- data/lib/bio-alignment/edit/mask_islands.rb +115 -0
- data/lib/bio-alignment/edit/mask_serial_mutations.rb +44 -0
- data/lib/bio-alignment/elements.rb +86 -0
- data/lib/bio-alignment/rows.rb +52 -0
- data/lib/bio-alignment/sequence.rb +20 -14
- data/lib/bio-alignment/state.rb +64 -8
- data/lib/bio-alignment/tree.rb +77 -0
- data/spec/bio-alignment_spec.rb +57 -1
- data/spec/spec_helper.rb +3 -3
- metadata +47 -22
- data/lib/bio-alignment/column.rb +0 -47
data/lib/bio-alignment/column.rb
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require 'bio-alignment/state'
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module Bio
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module BioAlignment
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# The Columns module provides accessors for the column list
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# returning Column objects
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module Columns
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# Return a list of Column objects. The contents of the
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# columns are accessed lazily
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def columns
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(0..num_columns-1).map { | col | Column.new(self,col) }
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end
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def num_columns
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rows.first.length
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end
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end
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# Support the notion of columns in an alignment. A column
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# can have state by attaching state objects
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class Column
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include State
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def initialize aln, col
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@aln = aln
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@col = col
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end
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def [] index
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@aln[index][@col]
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end
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# iterator fetches a column on demand
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def each
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@aln.each do | seq |
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yield seq[@col]
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end
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end
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end
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end
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end
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