bio-alignment 0.0.4 → 0.0.5

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - jruby-19mode # JRuby in 1.9 mode
+#  - 1.8.7
+#  - 1.9.3
+#  - rbx-19mode
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/README.md

@@ -41,9 +41,43 @@ aligmment (note codon gaps are represented by '---')
   end
 ```
 
+Now add some state - you can define your own row state
+
+```ruby
+  # tell the row to handle state
+  aln[0].extend(State)
+  # mark the first row for deletion
+  aln[0].state = MyStateDeleteObject.new
+  if aln.rows[0].state.deleted?
+    # do something
+  end
+```
+
+### Accessing columns
+
+BioAlignment has a module for handling columns in an alignment. As
+long as the contained sequence objects have the [] and length methods,
+they can lazily be iterated by column. To get a column and iterate it
+
+```ruby
+  column = aln.columns[3]
+  column.each do |element|
+    p element
+  end
+```
+
+Now add some state - you can define your own column state
+
+```ruby
+  aln.columns[3].state = MyStateDeleteObject.new
+  if aln.columns[3].state.deleted?
+    # do something
+  end
+```
+
 ### BioRuby Sequence objects
 
-The BioAlignment supports BioRuby's Bio::Sequence objects:
+BioAlignment supports adding BioRuby's Bio::Sequence objects:
 
 ```ruby
   require 'bio'  # BioRuby
@@ -54,6 +88,14 @@ The BioAlignment supports BioRuby's Bio::Sequence objects:
   aln << Bio::Sequence::NA.new("atg---tcaaaa")
 ```
 
+and we can transform BioAlignment into BioRuby's Bio::Alignment and
+use BioRuby functions
+
+```ruby
+  bioruby_aln = aln.to_bioruby_alignment
+  bioruby_aln.consensus_iupac
+```
+
 ### Pal2nal
 
 A protein (amino acid) to nucleotide alignment would first load
@@ -72,7 +114,7 @@ the sequences
   end
 ```
 
-Write a (simple) version of pal2nal would be something like
+Writing a (simple) version of pal2nal would be something like
 
 ```ruby
   fasta3 = FastaWriter.new('nt-aln.fa')
@@ -95,15 +137,33 @@ Write a (simple) version of pal2nal would be something like
   end
 ```
 
-With amino acid aln1 and nucleotide aln2 loaded, the library version
-includes validation, and is the shorter command 
+With amino acid aa_aln and nucleotide nt_aln loaded, the library
+version of pal2nal includes validation
 
 ```ruby
-  aln3 = aln1.pal2nal(aln2, :codon_table => 3)
+  aln = aa_aln.pal2nal(nt_aln, :codon_table => 3, :do_validate => true)
 ```
 
 resulting in the codon alignment.
 
+### Alignment editing
+
+BioAlignment supports multiple alignment editing features, which are
+listed
+[here](https://github.com/pjotrp/bioruby-alignment/tree/master/features/edit).
+Each edition feature is added at runtime(!) Example:
+
+```ruby
+  require 'bio-alignment/edit/del_bridges'
+
+  aln.extend DelBridges   # bring the module into scope
+  aln2 = aln.clean(50)    # execute the alignment editor
+```
+
+
+
+### See also
+
 The API documentation is online. For more code examples see
 [./spec/*.rb](https://github.com/pjotrp/bioruby-alignment/tree/master/spec) and
 [./features/*](https://github.com/pjotrp/bioruby-alignment/tree/master/features).

data/VERSION

@@ -1 +1 @@
-0.0.4
+0.0.5

data/doc/bio-alignment-design.md

@@ -22,13 +22,13 @@ say we have a nucleotide sequence with pay load
     5   9   *    1
 
 most library implementations will have two strings "AGTA" and "59*1".
-Removing the third nucleodide would mean removing it twice, into first
+Removing the third nucleotide would mean removing it twice, into first
 "AGA", and second "591". With bio-alignment this is one action because we
 have one object for each element that contains both values, e.g. the
 payload of 'T' is '*'. Moving 'T' automatically moves '*'.
 
 In addition the bio-alignment library deals with codons and codon translation.
-Rather than track mulitiple matrices, the codon is viewed as an element,
+Rather than track multiple matrices, the codon is viewed as an element,
 and the translated codon as the pay load. Again, when an alignment gets
 reordered the code only has to do it in one place.
 
@@ -89,7 +89,7 @@ do a fancy
 
 Elements in the list should respond to a gap? method, for an alignment
 gap, and the undefined? method for a position that is either an
-element or a gap. Also it should respont to the to_s method.
+element or a gap. Also it should respond to the to_s method.
 
 An element can contain any pay load.  If a list of attributes exists
 in the sequence object, it can be used.
@@ -100,6 +100,11 @@ The column list tracks the columns of the alignment. The requirement
 is that it should be iterable and can be indexed. The Column contains
 no elements, but may point to a list when the alignment is transposed.
 
+One of the 'features' of this library is that the Column access logic is 
+split out into a separate module, which accesses the data in a lazy fashion. 
+Also column state is stored as an 'any object'. I.e. a column can contain
+any state.
+
 ## Matrix or MSA
 
 The Matrix consists of a Column list, multiple Sequences, in turn
@@ -130,6 +135,26 @@ The Matrix can be accessed in transposed fashion, but accessing the normal
 matrix and transposed matrix at the same time is not supported.  Matrix is not
 designed to be transaction safe - though you can copy the Matrix any time.
 
+## Adding functionality
+
+To ascertain that the basic BioAlignment does not get polluted, extra functionality
+is added by Modules. These modules can be added at run time(!) One advantage is
+that there is less name space pollution, the other is that different implementations
+can be plugged in - using the same interface. For example, here we are going to
+use an alignment editor named DelBridges, which has a method named clean:
+
+```ruby
+  require 'bio-alignment/edit/del_bridges'
+
+  aln = Alignment.new(string.split(/\n/))
+  aln.extend DelBridges   # bring the module into scope
+  aln2 = aln.clean
+```
+
+in other words, the functionality in DelBridges gets attached to the aln
+instance at run time, without affecting any other Alignment object(!) Also,
+when not requiring 'bio-alignment/edit/del_bridges', the functionality is never
+visible, and never added to the environment.
 
 
 Copyright (C) 2012 Pjotr Prins <pjotr.prins@thebird.nl>

data/features/bioruby-feature.rb

@@ -67,14 +67,18 @@ end
 # ----
 
 Given /^I have a BioAlignment$/ do
-  pending # express the regexp above with the code you wish you had
+  @aln1 = Alignment.new
+  fasta = FastaReader.new('test/data/fasta/codon/aa-alignment.fa')
+  fasta.each do | rec |
+    @aln1.sequences << Sequence.new(rec.id, rec.seq)
+  end
 end
 
 When /^I convert$/ do
-  pending # express the regexp above with the code you wish you had
+  @bioruby_alignment = @aln1.to_bioruby_alignment
 end
 
-Then /^I should have a Bio::Alignment$/ do
-  pending # express the regexp above with the code you wish you had
+Then /^I should have a BioRuby Bio::Alignment$/ do
+  @bioruby_alignment.consensus_iupac[0..8].should == '???????v?'
 end
 

data/features/bioruby.feature

@@ -3,6 +3,7 @@ Feature: BioAlignment should play with BioRuby
   I want to convert BioAlignment to Bio::Alignment
   And I want to support Bio::Sequence objects
 
+  @bioruby
   Scenario: Use Bio::Sequence to fill BioAlignment
     Given I have multiple Bio::Sequence objects
     When I assign BioAlignment
@@ -17,7 +18,7 @@ Feature: BioAlignment should play with BioRuby
     And and return a partial AA sequence
     And be AA indexable
 
-  Scenario: Convert BioAlignment to Bio::Alignment
+  Scenario: Convert BioAlignment to BioRuby Bio::Alignment
     Given I have a BioAlignment
     When I convert
-    Then I should have a Bio::Alignment
+    Then I should have a BioRuby Bio::Alignment

data/features/columns-feature.rb

@@ -0,0 +1,33 @@
+Given /^I iterate the columns$/ do
+  @aln.should_not be_nil  # aln is loaded by codon-feature.rb
+end
+
+column = nil
+When /^I fetch a column$/ do
+  column = @aln.columns[3]
+  column.should_not be_nil
+  column[0].to_s.should == 'cga'
+end
+
+When /^I inject column state$/ do
+  column.state = ColumnState.new
+  column.state.deleted = true
+end
+
+Then /^I should be able to get the column state$/ do
+  column.state.deleted?.should be_true
+end
+
+list = []
+When /^I iterate a column$/ do
+  column10 = @aln.columns[10]
+  column10.each do | element | 
+    list << element.to_s
+  end
+end
+
+Then /^I should get the column elements$/ do
+  list[0..10].should == 
+  ["ctt", "gcg", "ctt", "ttt", "gcg", "ttt", "ttt", "agt", "ttt", "atg", "agt"]
+end
+

data/features/columns.feature

@@ -0,0 +1,14 @@
+Feature: Alignment column support
+  In order to access an alignment by column
+  I want to access column state
+  I want to get all elements in a column
+
+  @columns
+  Scenario: Access column information in an alignment
+    Given I read an MSA nucleotide FASTA file in the test/data folder
+    When I fetch a column
+    When I inject column state
+    Then I should be able to get the column state
+    When I iterate a column
+    Then I should get the column elements
+

data/features/edit/del_bridges-feature.rb

@@ -0,0 +1,21 @@
+require 'bio-alignment'
+require 'bio-alignment/edit/del_bridges'
+
+Given /^I have a bridged alignment$/ do |string|
+  @aln = Alignment.new(string.split(/\n/))
+end
+
+When /^I apply the bridge rule$/ do
+  @aln.extend DelBridges
+  aln2 = @aln.clean
+end
+
+Then /^it should have removed (\d+) bridges$/ do |arg1, string|
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^I should be able to track removed columns$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+

data/features/edit/del_bridges.feature

@@ -0,0 +1,36 @@
+Feature: Alignment editing, the bridge rule
+  Remove columns that contain too many gaps
+
+  Drop all bridges in less than 'min_bridges_fraction' (default 1/3 or 33%).
+
+  The dropped columns are tracked by the table columns.
+
+  @dev
+  Scenario: Apply bridge rule to an amino acid alignment
+    Given I have a bridged alignment
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      -------------IFHAVR-TC-HP-----------------
+      """
+    When I apply the bridge rule
+    Then it should have removed 4 bridges
+      """
+      SNSFSRPTIIFSGCSTACSGKSELVCGFRSFMLSDV
+      SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV
+      SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV
+      PKLFSRPTIIFSGCSTACSGKSEPVCGFRSFMLSDV
+      ------PTIIFSGCSKACSGKSELVCGFRSFMLSDV
+      ------PTIIFSGCSKACSGK---FRSFRSFMLSAV
+      ------PTIIFSGCSKACSGK---VCGIFHAVRSFM
+      ------PTIIFSGCSKACSGKSELVCGFRSFMLSAV
+      ---------IFHAVR-TC-HP---------------
+      """
+    Then I should be able to track removed columns
+

data/features/edit/del_non_informative_sequences.feature

@@ -0,0 +1,4 @@
+Feature: Remove non-informative sequences
+
+  After alignment cleaning, it may be we have non-informative sequences. These
+  can be removed from the alignment.

data/features/edit/gblocks-feature.rb

@@ -0,0 +1,13 @@
+When /^I apply GBlocks$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^it should return the GBlocks cleaned alignment$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^return a list of removed columns$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+

data/features/edit/gblocks.feature

@@ -0,0 +1,31 @@
+Feature: GBlocks implementation in Ruby
+
+  The GBlocks routine is often used, but the source code is not open source. This 
+  is a feature request for a reimplementation of GBlocks. Some links:
+
+  Open sourcing request by Debian: http://lists.debian.org/debian-med/2011/02/msg00008.html
+
+  Binary download of GBlocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
+
+  Documentation: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html
+
+  It is quite a simple routine, and would be easy to validate against existing outcomes.
+
+  Scenario: Apply GBlocks to an alignment
+    Given I have an alignment
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      -------------IFHAVR-TC-HP-----------------
+      """
+    When I apply GBlocks
+    Then it should return the GBlocks cleaned alignment
+    And return a list of removed columns
+
+

data/features/edit/mask_islands-feature.rb

@@ -0,0 +1,12 @@
+require 'bio-alignment'
+
+When /^I apply island rule with max_gap_size (\d+)$/ do |arg1|
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^it should result in$/ do |string|
+  pending # express the regexp above with the code you wish you had
+end
+
+
+

data/features/edit/mask_islands.feature

@@ -0,0 +1,44 @@
+Feature: Alignment editing with the Island rule
+  The idea is to drop hypervariable floating sequences, as they are probably
+  misaligned.
+
+  Drop all 'islands' in a sequence with low island consensus, that show a gap
+  larger than 'max_gap_size' (default 6) on both sides, and are shorter than
+  'min_island_size' (default 30). The latter may be a large size, as an island
+  needs to loop in and out several times to be (arguably) functional. We also
+  add a parameter 'max_gap_size_inside' (default 2) which allows for small gaps
+  inside the island - though the total island size is calculated including
+  those small gaps. 
+  
+  The island consensus is calculated by column.
+  'max_island_elements_unique_percentage' (default 10%) of elements in the
+  island should have a 'min_island_column_matched' (default 1) somewhere in the
+  element's column.
+
+  Scenario: Apply island rule to an amino acid alignment
+    Given I have an alignment
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      -------------IFHAVR-TC-HP-----------------
+      """
+    When I apply island rule with max_gap_size 4
+    Then it should have removed 2 islands
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----VCGFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----------------
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      ------------------------------------------
+      """
+

data/features/edit/mask_serial_mutations-feature.rb

@@ -0,0 +1,16 @@
+require 'bio-alignment'
+
+Given /^I have an alignment$/ do |string|
+  @aln = Alignment.new(string.split(/\n/))
+  p @aln
+end
+
+When /^I apply rule masking with X and max_gap_size (\d+)$/ do |arg1|
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^it should have removed (\d+) islands$/ do |arg1, string|
+  pending # express the regexp above with the code you wish you had
+end
+
+

data/features/edit/mask_serial_mutations.feature

@@ -0,0 +1,36 @@
+Feature: Alignment editing masking serial mutations
+  Edit an alignment removing or masking unique elements column-wise. 
+  
+  If a sequence has a unique AA in a column it is a single mutation event. If
+  multiple neighbouring AA's are also unique we suspect the sequence is an
+  outlier. This rule masks, or deletes, stretches of unique AAs. The stretch of
+  unique AA's is defined in 'max_serial_unique' (default 5, so two bordering
+  unique AA's are allowed).
+
+  Scenario: Apply rule to an amino acid alignment
+    Given I have an alignment
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACSQQKLTSEQVCFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      -------------IFHAVR-TC-HP-----------------
+      """
+    When I apply rule masking with X and max_gap_size 5
+    Then it should result in
+      """
+      ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
+      SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
+      SSIISNSFSRPTIIFSGCSTACXXXXXXXXXXXFR---LSDV
+      ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
+      ----------PTIIFSGCSKACSGK-----VCGFRSFMLSAV
+      ----------PTIIFSGCSKACSGK-----------------
+      ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
+      -------------XXXXXX-XX-XX-----------------
+      """
+

data/features/rows-feature.rb

@@ -0,0 +1,35 @@
+Given /^I iterate the rows$/ do
+  @aln.should_not be_nil  # aln is loaded by codon-feature.rb
+end
+
+row = nil
+When /^I fetch a row$/ do
+  row = @aln.rows[3]
+  row.should_not be_nil
+  row[0].to_s.should == '---'
+end
+
+When /^I inject row state$/ do
+  # tell row to handle state
+  row.extend(State)
+  row.state = RowState.new
+  row.state.deleted = true
+end
+
+Then /^I should be able to get the row state$/ do
+  row.state.deleted?.should be_true
+end
+
+list = []
+When /^I iterate a row$/ do
+  row10 = @aln.rows[10]
+  row10.each do | element | 
+    list << element.to_s
+  end
+end
+
+Then /^I should get the row elements$/ do
+  list[0..10].should == ["---", "---", "---", "---", "---", "---", "---", "atg", "tcg", "tcc", "agt"]
+
+end
+

data/features/rows.feature

@@ -0,0 +1,14 @@
+Feature: Alignment row support
+  In order to access an alignment by row
+  I want to access the row state
+
+  @rows
+  Scenario: Access row information in an alignment
+    Given I read an MSA nucleotide FASTA file in the test/data folder
+    When I fetch a row
+    When I inject row state
+    Then I should be able to get the row state
+    When I iterate a row
+    Then I should get the row elements
+
+

data/lib/bio-alignment/alignment.rb

@@ -1,6 +1,7 @@
 # Alignment
 
 require 'bio-alignment/pal2nal'
+require 'bio-alignment/column'
 
 module Bio
  
@@ -9,22 +10,37 @@ module Bio
     class Alignment
       include Enumerable
       include Pal2Nal
+      include Columns
 
       attr_accessor :sequences
 
-      def initialize
+      # Create alignment. seqs can be a list of sequences. If these
+      # are String types, they get converted to the library Sequence 
+      # container
+      def initialize seqs = nil
         @sequences = []
+        if seqs 
+          seqs.each_with_index do | seq, i |
+            @sequences << 
+              if seq.kind_of?(String)
+                Sequence.new(i,seq)
+              else
+                seq
+              end
+          end
+        end
       end
 
       alias rows sequences
 
-      # def [] index  <- need matrix
-      #   rows[index]
-      # end
+      def [] index
+        rows[index]
+      end
 
       def each
         rows.each { | seq | yield seq }
       end
+
     end
   end
 end

data/lib/bio-alignment/bioruby.rb

@@ -18,5 +18,14 @@ module Bio
       end
     end
   end
+
+  # Here we add a BioRuby converter
+  module BioAlignment
+    class Alignment
+      def to_bioruby_alignment
+        Bio::Alignment.new(self)
+      end
+    end
+  end
 end
 

data/lib/bio-alignment/codonsequence.rb

@@ -74,6 +74,10 @@ module Bio
         @seq[index]
       end
 
+      def length
+        @seq.length
+      end
+
       def each
         @seq.each { | codon | yield codon }
       end

data/lib/bio-alignment/column.rb

@@ -0,0 +1,47 @@
+require 'bio-alignment/state'
+
+module Bio
+ 
+  module BioAlignment
+
+    # The Columns module provides accessors for the column list
+    # returning Column objects
+    module Columns
+     
+      # Return a list of Column objects. The contents of the  
+      # columns are accessed lazily
+      def columns
+        (0..num_columns-1).map { | col | Column.new(self,col) }
+      end
+
+      def num_columns
+        rows.first.length
+      end
+    end
+
+    # Support the notion of columns in an alignment. A column
+    # can have state by attaching state objects
+    class Column
+      include State
+
+      def initialize aln, col
+        @aln = aln
+        @col = col
+      end
+
+      def [] index
+        @aln[index][@col] 
+      end
+
+      # iterator fetches a column on demand
+      def each
+        @aln.each do | seq |
+          yield seq[@col]
+        end
+      end
+    end
+
+  end
+
+end
+

data/lib/bio-alignment/edit/del_bridges.rb

@@ -0,0 +1,11 @@
+
+module Bio
+  module BioAlignment
+
+    module DelBridges
+   
+      def clean
+      end
+    end
+  end
+end

data/lib/bio-alignment/pal2nal.rb

@@ -3,17 +3,24 @@
 module Bio
   module BioAlignment
     module Pal2Nal
-      def pal2nal nt_aln, options = { :codon_table => 1 }
+
+      # Protein to nucleotide alignment, using a codon table for testing. If :do_validate is
+      # false, translation for validation is skipped (note CodonSequence translation is lazy).
+      def pal2nal nt_aln, options = { :codon_table => 1, :do_validate => true }
+        do_validate = options[:do_validate]
         aa_aln = self
         codon_aln = Alignment.new
         aa_aln.each_with_index do | aaseq, i |
           ntseq = nt_aln.sequences[i]
           raise "pal2nal sequence IDs do not match (for #{aaseq.id} != #{ntseq.id})" if aaseq.id != ntseq.id
           raise "pal2nal sequence size does not match (for #{aaseq.id}'s #{aaseq.to_s.size}!= #{ntseq.to_s.size * 3})" if aaseq.id != ntseq.id
+          # create a Codon sequence out of the nucleotide sequence (no gaps)
           codonseq = CodonSequence.new(ntseq.id, ntseq.seq, options)
 
           codon_pos = 0
           result = []
+
+          # now fill the result array by finding codons and gaps, and testing for valid amino acids
           aaseq.each do | aa |
             result <<
               if aa.gap?
@@ -21,11 +28,12 @@ module Bio
               else
                 codon = codonseq[codon_pos]
                 # validate codon translates to amino acid
-                raise "codon does not match amino acid (for #{aaseq.id}, position #{codon_pos}, #{codon} translates to #{codon.to_aa} instead of #{aa.to_s})" if codon.to_aa != aa.to_s
+                raise "codon does not match amino acid (for #{aaseq.id}, position #{codon_pos}, #{codon} translates to #{codon.to_aa} instead of #{aa.to_s})" if do_validate and codon.to_aa != aa.to_s
                 codon_pos += 1
                 codon.to_s
               end
           end
+          # the new result is transformed to a gapped CodonSequence
           codon_seq = CodonSequence.new(aaseq.id, result.join(''), options)
           codon_aln.sequences << codon_seq
         end

data/lib/bio-alignment/sequence.rb

@@ -18,6 +18,7 @@ module Bio
     #
     class Sequence
       include Enumerable
+      include State
 
       attr_reader :id, :seq
       def initialize id, seq
@@ -29,6 +30,10 @@ module Bio
         @seq[index]
       end
 
+      def length
+        @seq.length
+      end
+
       def each
         @seq.each_char { | c | yield Element.new(c) }
       end

data/lib/bio-alignment/state.rb

@@ -0,0 +1,31 @@
+module Bio
+ 
+  module BioAlignment
+
+    module State
+      attr_accessor :state
+    end
+
+    # Convenience class for tracking state. Note you can add
+    # any class you like
+    class ColumnState
+      attr_accessor :deleted
+
+      def deleted?
+        deleted == true
+      end
+    end
+
+    # Convenience class for tracking state. Note you can add
+    # any class you like
+    class RowState
+      attr_accessor :deleted
+
+      def deleted?
+        deleted == true
+      end
+    end
+
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-06 00:00:00.000000000Z
+date: 2012-02-28 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &16310560 !ruby/object:Gem::Requirement
+  requirement: &11633860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *16310560
+  version_requirements: *11633860
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &16309720 !ruby/object:Gem::Requirement
+  requirement: &11632600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *16309720
+  version_requirements: *11632600
 - !ruby/object:Gem::Dependency
   name: bio-bigbio
-  requirement: &16309060 !ruby/object:Gem::Requirement
+  requirement: &11622800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -43,10 +43,10 @@ dependencies:
         version: 0.1.3
   type: :development
   prerelease: false
-  version_requirements: *16309060
+  version_requirements: *11622800
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &16308000 !ruby/object:Gem::Requirement
+  requirement: &11622000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16308000
+  version_requirements: *11622000
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &16306500 !ruby/object:Gem::Requirement
+  requirement: &11621400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *16306500
+  version_requirements: *11621400
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &16305460 !ruby/object:Gem::Requirement
+  requirement: &11620480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *16305460
+  version_requirements: *11620480
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &16304680 !ruby/object:Gem::Requirement
+  requirement: &11619680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,7 +87,7 @@ dependencies:
         version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *16304680
+  version_requirements: *11619680
 description: Alignment handler for multiple sequence alignments (MSA)
 email: pjotr.public01@thebird.nl
 executables:
@@ -99,6 +99,7 @@ extra_rdoc_files:
 files:
 - .document
 - .rspec
+- .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -110,14 +111,30 @@ files:
 - features/bioruby.feature
 - features/codon-feature.rb
 - features/codon.feature
+- features/columns-feature.rb
+- features/columns.feature
+- features/edit/del_bridges-feature.rb
+- features/edit/del_bridges.feature
+- features/edit/del_non_informative_sequences.feature
+- features/edit/gblocks-feature.rb
+- features/edit/gblocks.feature
+- features/edit/mask_islands-feature.rb
+- features/edit/mask_islands.feature
+- features/edit/mask_serial_mutations-feature.rb
+- features/edit/mask_serial_mutations.feature
 - features/pal2nal-feature.rb
 - features/pal2nal.feature
+- features/rows-feature.rb
+- features/rows.feature
 - lib/bio-alignment.rb
 - lib/bio-alignment/alignment.rb
 - lib/bio-alignment/bioruby.rb
 - lib/bio-alignment/codonsequence.rb
+- lib/bio-alignment/column.rb
+- lib/bio-alignment/edit/del_bridges.rb
 - lib/bio-alignment/pal2nal.rb
 - lib/bio-alignment/sequence.rb
+- lib/bio-alignment/state.rb
 - spec/bio-alignment_spec.rb
 - spec/spec_helper.rb
 - test/data/fasta/codon/aa-alignment.fa
@@ -141,7 +158,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -237499918493109825
+      hash: 1565072942973090495
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: