bio-alignment 0.0.5 → 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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