bioseqalign 0.0.3 → 0.0.4

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.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA1:
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- data.tar.gz: 96d9c502f30a612eec662baeec5f0a275714e912
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+ metadata.gz: eebe247527833046b360916889bc3e443b58ad88
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+ data.tar.gz: 2627922393b2b810d35652fd1e4d8ecb73c83a89
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  SHA512:
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- metadata.gz: 792e24c7020440b3377f9c4f9218b21bdf5c986d582d2ffcf76f0292547d938353544fafe20b02fc2e0a9fe65e622736782e13ca8903807e2a5977c25e407206
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- data.tar.gz: fb8c79b054f34495d921307902e0554841e2771742065243912c4a8ff0bf332ede46b8ccbbdcd1cab60884a3575b61b8aa4df3bdf22242dc8a8fc2c027caf678
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+ metadata.gz: 38cedead4c547bbd32abe240de94f11ace65b67c9889ad1a7da33e70a5d83bab0a882844ab0031db401e7096b0644f887760b575f07b80a16428b74005a13687
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+ data.tar.gz: b763ec760284ec0ae8ed9733ea77d1f67260e15e67f9288eb49df48ad66d9835b479db4e94f5bb0a58ee665058040ac8a1437a3cd7e0e49d433d5d2d6ef3310a
@@ -13,10 +13,8 @@ Rice::Array LocalAlign::getAlignment() {
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  assignSource(row(ali, 1), seq2);
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  //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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- localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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-
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- //std::cout<<row(ali, 0)<<std::endl;
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- //std::cout<<row(ali, 1)<<std::endl;
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+ //localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore));
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  typedef Iterator<TRow>::Type TRowIterator;
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  TRowIterator it = begin(row(ali, 0));
@@ -34,10 +32,6 @@ Rice::Array LocalAlign::getAlignment() {
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  else s_row2 += (*it2);
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  }
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- // std::cout<<s_row1<<std::endl;
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- // std::cout<<s_row2<<std::endl;
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- // std::cout<<ali<<std::endl;
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-
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  return getArrayFromAlignStr(s_row1+s_row2);
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  }
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@@ -48,6 +42,7 @@ void LocalAlign::run() {
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  assignSource(row(ali, 0), seq1);
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  assignSource(row(ali, 1), seq2);
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- score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ //score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore));
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  }
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@@ -1,6 +1,6 @@
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1
 
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  module BioSeqAlign
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- VERSION='0.0.3'
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+ VERSION='0.0.4'
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  end
metadata CHANGED
@@ -1,29 +1,29 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bioseqalign
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  version: !ruby/object:Gem::Version
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- version: 0.0.3
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+ version: 0.0.4
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  platform: ruby
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  authors:
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  - Stefano R.B.
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-08-06 00:00:00.000000000 Z
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+ date: 2016-04-07 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rice
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '2.1'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '2.1'
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  description: A simple gem to perform fast pairwise sequence alignment using seqan
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  email: stefano.rb@gmail.com
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  executables: []
@@ -32,32 +32,17 @@ extensions:
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  extra_rdoc_files: []
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  files:
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  - ext/bioseqalign/FitAlign.cpp
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- - ext/bioseqalign/FitAlign.cpp~
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  - ext/bioseqalign/FitAlign.hpp
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- - ext/bioseqalign/FitAlign.hpp~
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  - ext/bioseqalign/GlobalAlign.cpp
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- - ext/bioseqalign/GlobalAlign.cpp~
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  - ext/bioseqalign/GlobalAlign.hpp
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- - ext/bioseqalign/GlobalAlign.hpp~
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  - ext/bioseqalign/LocalAlign.cpp
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- - ext/bioseqalign/LocalAlign.cpp~
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  - ext/bioseqalign/LocalAlign.hpp
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- - ext/bioseqalign/LocalAlign.hpp~
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- - ext/bioseqalign/Makefile
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  - ext/bioseqalign/PairwiseAlign.cpp
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- - ext/bioseqalign/PairwiseAlign.cpp~
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  - ext/bioseqalign/PairwiseAlign.hpp
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- - ext/bioseqalign/PairwiseAlign.hpp~
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  - ext/bioseqalign/PrefixSuffixAlign.cpp
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- - ext/bioseqalign/PrefixSuffixAlign.cpp~
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  - ext/bioseqalign/PrefixSuffixAlign.hpp
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- - ext/bioseqalign/PrefixSuffixAlign.hpp~
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  - ext/bioseqalign/extconf.rb
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- - ext/bioseqalign/extconf.rb~
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  - ext/bioseqalign/fitalgntest.cpp
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- - ext/bioseqalign/fitalgntest.cpp~
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- - ext/bioseqalign/runTest.rb
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- - ext/bioseqalign/runTest.rb~
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  - lib/bioseqalign.rb
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  - lib/bioseqalign/version.rb
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  homepage: https://github.com/stefrb/bioseqalign
@@ -71,17 +56,17 @@ require_paths:
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  - ext
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  required_ruby_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: '0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.4.3
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+ rubygems_version: 2.2.2
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  signing_key:
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  specification_version: 4
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  summary: Pairwise sequence alignment using seqan
@@ -1,42 +0,0 @@
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- #include "FitAlign.hpp"
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-
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- FitAlign::FitAlign() {}
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-
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- FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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-
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- // unable to figure out how to properly overload constructor using RICE
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- //FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
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-
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- std::string FitAlign::getAlignment() {
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- TSequence tseq1 = seq1;
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- TSequence tseq2 = seq2;
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-
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- TStringSet sequences;
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- appendValue(sequences,tseq1);
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- appendValue(sequences,tseq2);
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-
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- TAlignGraph alignG(sequences);
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-
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- // don't penalize gaps on begin/end of seq2
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- globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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-
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- std::stringstream ss;
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- ss<<alignG;
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- return ss.str();
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- }
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-
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-
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- void FitAlign::run() {
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- TSequence tseq1 = seq1;
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- TSequence tseq2 = seq2;
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-
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- TStringSet sequences;
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- appendValue(sequences,tseq1);
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- appendValue(sequences,tseq2);
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-
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- TAlignGraph alignG(sequences);
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-
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- // don't penalize gaps on begin/end of seq2
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- score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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-
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- }
@@ -1,20 +0,0 @@
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- #include <iostream>
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- #include <string>
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- #include <seqan/align.h>
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-
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- #include "PairwiseAlign.hpp"
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-
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- using namespace seqan;
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-
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- class FitAlign : public PairwiseAlign {
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- public:
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- FitAlign();
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- FitAlign(std::string s1, std::string s2);
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- //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
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- virtual ~FitAlign() {}
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-
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- virtual void run();
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- virtual std::string getAlignment();
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-
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- };
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-
@@ -1,53 +0,0 @@
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- // global alignment
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-
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- #include "GlobalAlign.hpp"
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-
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- GlobalAlign::GlobalAlign() {}
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-
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- GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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-
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- Rice::Array GlobalAlign::getAlignment() {
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- TAlign ali;
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- resize(rows(ali), 2);
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- assignSource(row(ali, 0), seq1);
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- assignSource(row(ali, 1), seq2);
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-
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- //globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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- globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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-
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- //std::cout<<row(ali, 0)<<std::endl;
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- //std::cout<<row(ali, 1)<<std::endl;
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-
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- typedef Iterator<TRow>::Type TRowIterator;
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- TRowIterator it = begin(row(ali, 0));
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- TRowIterator itEnd = end(row(ali, 0));
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- std::string s_row1 = "";
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- for(; it != itEnd; ++it) {
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- if(isGap(it)) s_row1 += "-";
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- else s_row1 += (*it);
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- }
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- TRowIterator it2 = begin(row(ali, 1));
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- TRowIterator itEnd2 = end(row(ali, 1));
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- std::string s_row2 = "";
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- for(; it2 != itEnd2; ++it2) {
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- if(isGap(it2)) s_row2 += "-";
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- else s_row2 += (*it2);
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- }
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-
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- // std::cout<<s_row1<<std::endl;
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- // std::cout<<s_row2<<std::endl;
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- // std::cout<<ali<<std::endl;
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-
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- return getArrayFromAlignStr(s_row1+s_row2);
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- }
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-
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-
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- void GlobalAlign::run() {
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- TAlign ali;
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- resize(rows(ali), 2);
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- assignSource(row(ali, 0), seq1);
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- assignSource(row(ali, 1), seq2);
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-
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- score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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- }
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-
@@ -1,53 +0,0 @@
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- // local alignment
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-
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- #include "LocalAlign.hpp"
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-
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- LocalAlign::LocalAlign() {}
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-
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- LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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-
9
- Rice::Array LocalAlign::getAlignment() {
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- TAlign ali;
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- resize(rows(ali), 2);
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- assignSource(row(ali, 0), seq1);
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- assignSource(row(ali, 1), seq2);
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-
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- //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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- localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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-
18
- //std::cout<<row(ali, 0)<<std::endl;
19
- //std::cout<<row(ali, 1)<<std::endl;
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-
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- typedef Iterator<TRow>::Type TRowIterator;
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- TRowIterator it = begin(row(ali, 0));
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- TRowIterator itEnd = end(row(ali, 0));
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- std::string s_row1 = "";
25
- for(; it != itEnd; ++it) {
26
- if(isGap(it)) s_row1 += "-";
27
- else s_row1 += (*it);
28
- }
29
- TRowIterator it2 = begin(row(ali, 1));
30
- TRowIterator itEnd2 = end(row(ali, 1));
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- std::string s_row2 = "";
32
- for(; it2 != itEnd2; ++it2) {
33
- if(isGap(it2)) s_row2 += "-";
34
- else s_row2 += (*it2);
35
- }
36
-
37
- // std::cout<<s_row1<<std::endl;
38
- // std::cout<<s_row2<<std::endl;
39
- // std::cout<<ali<<std::endl;
40
-
41
- return getArrayFromAlignStr(s_row1+s_row2);
42
- }
43
-
44
-
45
- void LocalAlign::run() {
46
- TAlign ali;
47
- resize(rows(ali), 2);
48
- assignSource(row(ali, 0), seq1);
49
- assignSource(row(ali, 1), seq2);
50
-
51
- score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
52
- }
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-
@@ -1 +0,0 @@
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- // local alignment
@@ -1 +0,0 @@
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- // local alignment
@@ -1,314 +0,0 @@
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-
2
- SHELL = /bin/sh
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-
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- # V=0 quiet, V=1 verbose. other values don't work.
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- V = 0
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- Q1 = $(V:1=)
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- Q = $(Q1:0=@)
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- ECHO1 = $(V:1=@:)
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- ECHO = $(ECHO1:0=@echo)
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- NULLCMD = :
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-
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- #### Start of system configuration section. ####
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-
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- srcdir = .
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- topdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0
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- hdrdir = $(topdir)
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- arch_hdrdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0/x86_64-linux
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- PATH_SEPARATOR = :
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- VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
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-
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- prefix = $(DESTDIR)/home/stef/.rvm/rubies/ruby-2.2.0
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-
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- rubysitearchprefix = $(rubylibprefix)/$(sitearch)
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-
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- rubyarchprefix = $(rubylibprefix)/$(arch)
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-
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- rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
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-
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- exec_prefix = $(prefix)
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-
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- vendorarchhdrdir = $(vendorhdrdir)/$(sitearch)
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-
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- sitearchhdrdir = $(sitehdrdir)/$(sitearch)
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-
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- rubyarchhdrdir = $(rubyhdrdir)/$(arch)
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-
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- vendorhdrdir = $(rubyhdrdir)/vendor_ruby
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-
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- sitehdrdir = $(rubyhdrdir)/site_ruby
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-
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- rubyhdrdir = $(includedir)/$(RUBY_VERSION_NAME)
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-
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- vendorarchdir = $(vendorlibdir)/$(sitearch)
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-
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- vendorlibdir = $(vendordir)/$(ruby_version)
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-
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- vendordir = $(rubylibprefix)/vendor_ruby
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-
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- sitearchdir = $(sitelibdir)/$(sitearch)
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-
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- sitelibdir = $(sitedir)/$(ruby_version)
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-
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- sitedir = $(rubylibprefix)/site_ruby
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-
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- rubyarchdir = $(rubylibdir)/$(arch)
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-
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- rubylibdir = $(rubylibprefix)/$(ruby_version)
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-
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- sitearchincludedir = $(includedir)/$(sitearch)
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-
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- archincludedir = $(includedir)/$(arch)
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-
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- sitearchlibdir = $(libdir)/$(sitearch)
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-
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- archlibdir = $(libdir)/$(arch)
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-
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- ridir = $(datarootdir)/$(RI_BASE_NAME)
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-
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- mandir = $(datarootdir)/man
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-
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- localedir = $(datarootdir)/locale
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-
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- libdir = $(exec_prefix)/lib
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-
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- psdir = $(docdir)
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-
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- pdfdir = $(docdir)
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-
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- dvidir = $(docdir)
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-
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- htmldir = $(docdir)
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-
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- infodir = $(datarootdir)/info
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-
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- docdir = $(datarootdir)/doc/$(PACKAGE)
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-
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- oldincludedir = $(DESTDIR)/usr/include
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-
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- includedir = $(prefix)/include
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-
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- localstatedir = $(prefix)/var
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-
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- sharedstatedir = $(prefix)/com
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-
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- sysconfdir = $(DESTDIR)/etc
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-
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- datadir = $(datarootdir)
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-
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- datarootdir = $(prefix)/share
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-
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- libexecdir = $(exec_prefix)/libexec
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-
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- sbindir = $(exec_prefix)/sbin
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-
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- bindir = $(exec_prefix)/bin
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-
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- archdir = $(rubyarchdir)
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-
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-
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-
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- CC = gcc
112
- CXX = g++
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- LIBRUBY = $(LIBRUBY_SO)
114
- LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
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- LIBRUBYARG_SHARED = -Wl,-rpath,'$${ORIGIN}/../lib' -Wl,-R'$${ORIGIN}/../lib' -l$(RUBY_SO_NAME)
116
- LIBRUBYARG_STATIC = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby-static
117
- empty =
118
- OUTFLAG = -o $(empty)
119
- COUTFLAG = -o $(empty)
120
-
121
- RUBY_EXTCONF_H =
122
- cflags = $(optflags) $(debugflags) $(warnflags)
123
- optflags = -O3 -fno-fast-math
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- debugflags = -ggdb3
125
- warnflags = -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration -Wdeprecated-declarations -Wno-packed-bitfield-compat
126
- CCDLFLAGS = -fPIC
127
- CFLAGS = $(CCDLFLAGS) $(cflags) -fPIC $(ARCH_FLAG)
128
- INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
129
- DEFS =
130
- CPPFLAGS = -I/home/stef/git_repos/tilapia/ext/seqan-1.3.1/ $(DEFS) $(cppflags) -I/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/include -std=c++11 -Wno-deprecated -Wno-unused-local-typedefs -Wimplicit-function-declaration -Wdeclaration-after-statement
131
- CXXFLAGS = $(CFLAGS) -Wall -g
132
- ldflags = -L. -fstack-protector -rdynamic -Wl,-export-dynamic -L/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/lib -lrice
133
- dldflags =
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- ARCH_FLAG =
135
- DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
136
- LDSHARED = g++ -shared
137
- LDSHAREDXX = $(CXX) -shared
138
- AR = ar
139
- EXEEXT =
140
-
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-
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- RUBY_INSTALL_NAME = $(RUBY_BASE_NAME)
143
-
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- RUBY_SO_NAME = ruby
145
-
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- RUBYW_INSTALL_NAME =
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-
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- RUBY_VERSION_NAME = $(RUBY_BASE_NAME)-$(ruby_version)
149
-
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- RUBYW_BASE_NAME = rubyw
151
-
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- RUBY_BASE_NAME = ruby
153
-
154
-
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- arch = x86_64-linux
156
- sitearch = $(arch)
157
- ruby_version = 2.2.0
158
- ruby = $(bindir)/$(RUBY_BASE_NAME)
159
- RUBY = $(ruby)
160
- ruby_headers = $(hdrdir)/ruby.h $(hdrdir)/ruby/ruby.h $(hdrdir)/ruby/defines.h $(hdrdir)/ruby/missing.h $(hdrdir)/ruby/intern.h $(hdrdir)/ruby/st.h $(hdrdir)/ruby/subst.h $(arch_hdrdir)/ruby/config.h
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-
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- RM = rm -f
163
- RM_RF = $(RUBY) -run -e rm -- -rf
164
- RMDIRS = rmdir --ignore-fail-on-non-empty -p
165
- MAKEDIRS = /bin/mkdir -p
166
- INSTALL = /usr/bin/install
167
- INSTALL_PROG = $(INSTALL) -m 0755
168
- INSTALL_DATA = $(INSTALL) -m 644
169
- COPY = cp
170
- TOUCH = exit >
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-
172
- #### End of system configuration section. ####
173
-
174
- preload =
175
-
176
-
177
- CXX = g++
178
-
179
- libpath = . $(libdir)
180
- LIBPATH = -L. -L$(libdir) -Wl,-R$(libdir)
181
- DEFFILE =
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-
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- CLEANFILES = mkmf.log
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- DISTCLEANFILES =
185
- DISTCLEANDIRS =
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-
187
- extout =
188
- extout_prefix =
189
- target_prefix =
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- LOCAL_LIBS =
191
- LIBS = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby -lpthread -ldl -lcrypt -lm -lc
192
- ORIG_SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
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- SRCS = $(ORIG_SRCS)
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- OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
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- HDRS = $(srcdir)/FitAlign.hpp $(srcdir)/GlobalAlign.hpp $(srcdir)/PrefixSuffixAlign.hpp $(srcdir)/LocalAlign.hpp $(srcdir)/PairwiseAlign.hpp
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- TARGET = SeqAlign
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- TARGET_NAME = SeqAlign
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- TARGET_ENTRY = Init_$(TARGET_NAME)
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- DLLIB = $(TARGET).so
200
- EXTSTATIC =
201
- STATIC_LIB =
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-
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- TIMESTAMP_DIR = .
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- BINDIR = $(bindir)
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- RUBYCOMMONDIR = $(sitedir)$(target_prefix)
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- RUBYLIBDIR = $(sitelibdir)$(target_prefix)
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- RUBYARCHDIR = $(sitearchdir)$(target_prefix)
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- HDRDIR = $(rubyhdrdir)/ruby$(target_prefix)
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- ARCHHDRDIR = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
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-
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- TARGET_SO = $(DLLIB)
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- CLEANLIBS = $(TARGET).so
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- CLEANOBJS = *.o *.bak
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-
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- all: $(DLLIB)
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- static: $(STATIC_LIB)
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- .PHONY: all install static install-so install-rb
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- .PHONY: clean clean-so clean-static clean-rb
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-
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- clean-static::
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- clean-rb-default::
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- clean-rb::
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- clean-so::
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- clean: clean-so clean-static clean-rb-default clean-rb
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- -$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
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-
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- distclean-rb-default::
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- distclean-rb::
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- distclean-so::
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- distclean-static::
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- distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
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- -$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
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- -$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
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- -$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
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-
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- realclean: distclean
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- install: install-so install-rb
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-
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- install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
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- $(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
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- clean-static::
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- -$(Q)$(RM) $(STATIC_LIB)
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- install-rb: pre-install-rb install-rb-default
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- install-rb-default: pre-install-rb-default
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- pre-install-rb: Makefile
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- pre-install-rb-default: Makefile
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- pre-install-rb-default:
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- @$(NULLCMD)
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- $(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
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- $(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
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- $(Q) $(TOUCH) $@
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-
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- site-install: site-install-so site-install-rb
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- site-install-so: install-so
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- site-install-rb: install-rb
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-
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- .SUFFIXES: .c .m .cc .mm .cxx .cpp .o .S
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-
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- .cc.o:
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- $(ECHO) compiling $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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-
263
- .cc.S:
264
- $(ECHO) translating $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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-
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- .mm.o:
268
- $(ECHO) compiling $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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-
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- .mm.S:
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- $(ECHO) translating $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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-
275
- .cxx.o:
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- $(ECHO) compiling $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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-
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- .cxx.S:
280
- $(ECHO) translating $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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-
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- .cpp.o:
284
- $(ECHO) compiling $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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-
287
- .cpp.S:
288
- $(ECHO) translating $(<)
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- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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-
291
- .c.o:
292
- $(ECHO) compiling $(<)
293
- $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
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-
295
- .c.S:
296
- $(ECHO) translating $(<)
297
- $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
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-
299
- .m.o:
300
- $(ECHO) compiling $(<)
301
- $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
302
-
303
- .m.S:
304
- $(ECHO) translating $(<)
305
- $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
306
-
307
- $(DLLIB): $(OBJS) Makefile
308
- $(ECHO) linking shared-object $(DLLIB)
309
- -$(Q)$(RM) $(@)
310
- $(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
311
-
312
-
313
-
314
- $(OBJS): $(HDRS) $(ruby_headers)
@@ -1,23 +0,0 @@
1
- #include "PairwiseAlign.hpp"
2
-
3
- PairwiseAlign::PairwiseAlign() {}
4
-
5
- PairwiseAlign::PairwiseAlign(std::string s1, std::string s2) {
6
- seq1 = s1;
7
- seq2 = s2;
8
- score = -10000;
9
- matchScore = 1;
10
- mismatchScore = -1;
11
- indelScore = -1;
12
- }
13
-
14
- // unable to properly figure out how to overload constructor when using RICE
15
- // PairwiseAlign::PairwiseAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) {
16
- // seq1 = s1;
17
- // seq2 = s2;
18
- // score = -10000;
19
- // matchScore = matchS;
20
- // mismatchScore = mismatchS;
21
- // indelScore = indelS;
22
- // }
23
-
@@ -1,54 +0,0 @@
1
- #ifndef PAIRWISE_ALIGN_HPP
2
- #define PAIRWISE_ALIGN_HPP
3
-
4
- #include <iostream>
5
- #include <string>
6
- #include <seqan/align.h>
7
-
8
- #include "rice/String.hpp"
9
- #include "rice/Array.hpp"
10
-
11
- using namespace seqan;
12
-
13
- typedef String<char> TSequence; // sequence type
14
- typedef StringSet<TSequence> TStringSet; // container for strings
15
- typedef StringSet<TSequence, Dependent<> > TDepStringSet; // dependent string set
16
- typedef Graph<Alignment<TDepStringSet> > TAlignGraph; // alignment graph
17
-
18
- typedef Align<TSequence,ArrayGaps> TAlign;
19
- typedef Row<TAlign>::Type TRow;
20
-
21
- class PairwiseAlign {
22
- protected:
23
- std::string seq1;
24
- std::string seq2;
25
- int score;
26
- TAlignGraph alignG;
27
- int matchScore;
28
- int mismatchScore;
29
- int indelScore;
30
- // return a ruby array of the alignment matrix string
31
- Rice::Array getArrayFromAlignStr(std::string alignMat);
32
-
33
- public:
34
- PairwiseAlign();
35
- PairwiseAlign(std::string s1, std::string s2);
36
- //PairwiseAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
37
- virtual ~PairwiseAlign() {}
38
-
39
- virtual void run() {}
40
- int getAlignScore() { return score; }
41
- //virtual std::string getAlignment() { return ""; }
42
- virtual Rice::Array getAlignment() { Rice::Array tmp; return tmp; }
43
-
44
- void setMatchScore(int mS) { matchScore = mS; }
45
- void setMismatchScore(int mS) { mismatchScore = mS; }
46
- void setIndelScore(int idS) { indelScore = idS; }
47
-
48
- std::string getSeq1() { return seq1; }
49
- std::string getSeq2() { return seq2; }
50
-
51
- };
52
-
53
-
54
- #endif
@@ -1,42 +0,0 @@
1
- #include "PrefixSuffixAlign.hpp"
2
-
3
- PrefixSuffixAlign::PrefixSuffixAlign() {}
4
-
5
- PrefixSuffixAlign::PrefixSuffixAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
6
-
7
- // unable to figure out how to properly overload constructor using RICE
8
- //PrefixSuffixAlign::PrefixSuffixAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
9
-
10
- std::string PrefixSuffixAlign::getAlignment() {
11
- TSequence tseq1 = seq1;
12
- TSequence tseq2 = seq2;
13
-
14
- TStringSet sequences;
15
- appendValue(sequences,tseq1);
16
- appendValue(sequences,tseq2);
17
-
18
- TAlignGraph alignG(sequences);
19
-
20
- // don't penalize gaps on begin/end of seq2
21
- globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
22
-
23
- std::stringstream ss;
24
- ss<<alignG;
25
- return ss.str();
26
- }
27
-
28
-
29
- void PrefixSuffixAlign::run() {
30
- TSequence tseq1 = seq1;
31
- TSequence tseq2 = seq2;
32
-
33
- TStringSet sequences;
34
- appendValue(sequences,tseq1);
35
- appendValue(sequences,tseq2);
36
-
37
- TAlignGraph alignG(sequences);
38
-
39
- // don't penalize gaps on begin/end of seq2
40
- score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
41
-
42
- }
@@ -1,20 +0,0 @@
1
- #include <iostream>
2
- #include <string>
3
- #include <seqan/align.h>
4
-
5
- #include "PairwiseAlign.hpp"
6
-
7
- using namespace seqan;
8
-
9
- class PrefixSuffixAlign : public PairwiseAlign {
10
- public:
11
- FitAlign();
12
- FitAlign(std::string s1, std::string s2);
13
- //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
14
- virtual ~FitAlign() {}
15
-
16
- virtual void run();
17
- virtual std::string getAlignment();
18
-
19
- };
20
-
@@ -1,2 +0,0 @@
1
- require 'mkmf-rice'
2
- create_makefile('FitAlign')
@@ -1,37 +0,0 @@
1
- #include "rice/Data_Type.hpp"
2
- #include "rice/Constructor.hpp"
3
- //#include "PairwiseAlign.hpp"
4
- #include "FitAlign.hpp"
5
- #include "PrefixSuffixAlign.hpp"
6
- using namespace Rice;
7
-
8
- extern "C"
9
-
10
- //void Init_FitAlign()
11
- void Init_SeqAlign()
12
- {
13
- Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class<PairwiseAlign>("PairwiseAlign")
14
- .define_constructor(Constructor<PairwiseAlign>())
15
- .define_constructor(Constructor<PairwiseAlign,std::string,std::string>())
16
- //.define_constructor(Constructor<PairwiseAlign,std::string,std::string,int,int,int>())
17
- .define_method("getAlignScore", &PairwiseAlign::getAlignScore)
18
- .define_method("getSeq1", &PairwiseAlign::getSeq1)
19
- .define_method("getSeq2", &PairwiseAlign::getSeq2)
20
- .define_method("run", &PairwiseAlign::run)
21
- .define_method("getAlignment", &PairwiseAlign::getAlignment)
22
- .define_method("setMatchScore", &PairwiseAlign::setMatchScore)
23
- .define_method("setMismatchScore", &PairwiseAlign::setMismatchScore)
24
- .define_method("setIndelScore", &PairwiseAlign::setIndelScore);
25
- Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
26
- .define_constructor(Constructor<FitAlign>())
27
- .define_constructor(Constructor<FitAlign,std::string,std::string>())
28
- //.define_constructor(Constructor<FitAlign,std::string,std::string,int,int,int>())
29
- .define_method("run", &FitAlign::run)
30
- .define_method("getAlignment", &FitAlign::getAlignment);
31
- Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
32
- .define_constructor(Constructor<PrefixSuffixAlign>())
33
- .define_constructor(Constructor<PrefixSuffixAlign,std::string,std::string>())
34
- .define_method("run", &PrefixSuffixAlign::run)
35
- .define_method("getAlignment", &PrefixSuffixAlign::getAlignment);
36
- //.define_method("getAlignmentArray", &PrefixSuffixAlign::getAlignmentArray);
37
- }
@@ -1,35 +0,0 @@
1
- require './SeqAlign'
2
-
3
-
4
- module BSA
5
-
6
- include SeqAlign
7
-
8
- end
9
-
10
- fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
11
- fa.run
12
- puts fa.getAlignScore
13
-
14
- #fa = SeqAlign::FitAlign.new("AAAACCCAAA", "CCC")
15
- #puts fa
16
- #fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
17
-
18
-
19
- Process.exit(0)
20
-
21
- require './SeqAlign'
22
-
23
- sa = PairwiseAlign.new("TCGA", "TCGA")
24
- puts sa.getSeq1
25
-
26
- #__END__
27
- fa = FitAlign.new("AAAAAAAATCGAGGG", "TCGA")
28
- fa.setMatchScore(2)
29
- fa.setMismatchScore(-1)
30
- fa.setIndelScore(-1)
31
- puts fa.getSeq1
32
- fa.run
33
- puts fa.getAlignScore
34
- puts fa.getAlignment
35
-
@@ -1,8 +0,0 @@
1
- require './FitAlign'
2
-
3
- fa = FitAlign.new("TCGA", "TCGA")
4
- puts fa.getSeq1
5
- fa.run
6
- puts fa.getAlignScore
7
- puts fa.getAlignment
8
-