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 +4 -4
- data/ext/bioseqalign/LocalAlign.cpp +4 -9
- data/lib/bioseqalign/version.rb +1 -1
- metadata +9 -24
- data/ext/bioseqalign/FitAlign.cpp~ +0 -42
- data/ext/bioseqalign/FitAlign.hpp~ +0 -20
- data/ext/bioseqalign/GlobalAlign.cpp~ +0 -53
- data/ext/bioseqalign/GlobalAlign.hpp~ +0 -53
- data/ext/bioseqalign/LocalAlign.cpp~ +0 -1
- data/ext/bioseqalign/LocalAlign.hpp~ +0 -1
- data/ext/bioseqalign/Makefile +0 -314
- data/ext/bioseqalign/PairwiseAlign.cpp~ +0 -23
- data/ext/bioseqalign/PairwiseAlign.hpp~ +0 -54
- data/ext/bioseqalign/PrefixSuffixAlign.cpp~ +0 -42
- data/ext/bioseqalign/PrefixSuffixAlign.hpp~ +0 -20
- data/ext/bioseqalign/extconf.rb~ +0 -2
- data/ext/bioseqalign/fitalgntest.cpp~ +0 -37
- data/ext/bioseqalign/runTest.rb +0 -35
- data/ext/bioseqalign/runTest.rb~ +0 -8
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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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:
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data.tar.gz:
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metadata.gz: 38cedead4c547bbd32abe240de94f11ace65b67c9889ad1a7da33e70a5d83bab0a882844ab0031db401e7096b0644f887760b575f07b80a16428b74005a13687
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data.tar.gz: b763ec760284ec0ae8ed9733ea77d1f67260e15e67f9288eb49df48ad66d9835b479db4e94f5bb0a58ee665058040ac8a1437a3cd7e0e49d433d5d2d6ef3310a
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@@ -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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//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));
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@@ -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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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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data/lib/bioseqalign/version.rb
CHANGED
metadata
CHANGED
@@ -1,29 +1,29 @@
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--- !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.
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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:
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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: '
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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: '
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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: []
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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
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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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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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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
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@@ -1,42 +0,0 @@
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#include "FitAlign.hpp"
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FitAlign::FitAlign() {}
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FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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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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std::string FitAlign::getAlignment() {
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TSequence tseq1 = seq1;
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TSequence tseq2 = seq2;
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TStringSet sequences;
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appendValue(sequences,tseq1);
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appendValue(sequences,tseq2);
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TAlignGraph alignG(sequences);
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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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std::stringstream ss;
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ss<<alignG;
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return ss.str();
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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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TStringSet sequences;
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appendValue(sequences,tseq1);
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appendValue(sequences,tseq2);
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TAlignGraph alignG(sequences);
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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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#include <iostream>
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#include <string>
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#include <seqan/align.h>
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#include "PairwiseAlign.hpp"
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using namespace seqan;
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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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virtual void run();
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virtual std::string getAlignment();
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};
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// global alignment
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#include "GlobalAlign.hpp"
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GlobalAlign::GlobalAlign() {}
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GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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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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//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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//std::cout<<row(ali, 0)<<std::endl;
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//std::cout<<row(ali, 1)<<std::endl;
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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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// 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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return getArrayFromAlignStr(s_row1+s_row2);
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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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score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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}
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// local alignment
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#include "LocalAlign.hpp"
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LocalAlign::LocalAlign() {}
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LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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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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//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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//std::cout<<row(ali, 0)<<std::endl;
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//std::cout<<row(ali, 1)<<std::endl;
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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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}
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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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// 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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return getArrayFromAlignStr(s_row1+s_row2);
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}
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void LocalAlign::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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score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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}
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// local alignment
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// local alignment
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data/ext/bioseqalign/Makefile
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SHELL = /bin/sh
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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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#### Start of system configuration section. ####
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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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prefix = $(DESTDIR)/home/stef/.rvm/rubies/ruby-2.2.0
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rubysitearchprefix = $(rubylibprefix)/$(sitearch)
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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
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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
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|
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LDSHAREDXX = $(CXX) -shared
|
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AR = ar
|
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EXEEXT =
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|
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|
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|
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|
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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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RM = rm -f
|
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RM_RF = $(RUBY) -run -e rm -- -rf
|
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RMDIRS = rmdir --ignore-fail-on-non-empty -p
|
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MAKEDIRS = /bin/mkdir -p
|
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INSTALL = /usr/bin/install
|
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INSTALL_PROG = $(INSTALL) -m 0755
|
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INSTALL_DATA = $(INSTALL) -m 644
|
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COPY = cp
|
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TOUCH = exit >
|
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|
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|
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#### End of system configuration section. ####
|
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|
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|
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preload =
|
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CXX = g++
|
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libpath = . $(libdir)
|
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|
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DEFFILE =
|
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|
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CLEANFILES = mkmf.log
|
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|
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DISTCLEANDIRS =
|
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|
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extout =
|
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extout_prefix =
|
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|
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target_prefix =
|
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|
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LOCAL_LIBS =
|
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|
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LIBS = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby -lpthread -ldl -lcrypt -lm -lc
|
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|
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ORIG_SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
|
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|
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SRCS = $(ORIG_SRCS)
|
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|
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OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
|
195
|
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HDRS = $(srcdir)/FitAlign.hpp $(srcdir)/GlobalAlign.hpp $(srcdir)/PrefixSuffixAlign.hpp $(srcdir)/LocalAlign.hpp $(srcdir)/PairwiseAlign.hpp
|
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|
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TARGET = SeqAlign
|
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|
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TARGET_NAME = SeqAlign
|
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|
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TARGET_ENTRY = Init_$(TARGET_NAME)
|
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|
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DLLIB = $(TARGET).so
|
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|
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EXTSTATIC =
|
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|
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STATIC_LIB =
|
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|
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|
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|
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TIMESTAMP_DIR = .
|
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|
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BINDIR = $(bindir)
|
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|
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RUBYCOMMONDIR = $(sitedir)$(target_prefix)
|
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|
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RUBYLIBDIR = $(sitelibdir)$(target_prefix)
|
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|
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RUBYARCHDIR = $(sitearchdir)$(target_prefix)
|
208
|
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HDRDIR = $(rubyhdrdir)/ruby$(target_prefix)
|
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|
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ARCHHDRDIR = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
|
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|
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|
211
|
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TARGET_SO = $(DLLIB)
|
212
|
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CLEANLIBS = $(TARGET).so
|
213
|
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CLEANOBJS = *.o *.bak
|
214
|
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|
215
|
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all: $(DLLIB)
|
216
|
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static: $(STATIC_LIB)
|
217
|
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.PHONY: all install static install-so install-rb
|
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|
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.PHONY: clean clean-so clean-static clean-rb
|
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|
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|
220
|
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clean-static::
|
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|
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clean-rb-default::
|
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|
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clean-rb::
|
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|
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clean-so::
|
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|
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clean: clean-so clean-static clean-rb-default clean-rb
|
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|
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-$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
|
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|
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|
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|
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distclean-rb-default::
|
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|
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distclean-rb::
|
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|
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distclean-so::
|
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|
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distclean-static::
|
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|
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distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
|
232
|
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-$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
|
233
|
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-$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
|
234
|
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-$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
|
235
|
-
|
236
|
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realclean: distclean
|
237
|
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install: install-so install-rb
|
238
|
-
|
239
|
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install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
|
240
|
-
$(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
|
241
|
-
clean-static::
|
242
|
-
-$(Q)$(RM) $(STATIC_LIB)
|
243
|
-
install-rb: pre-install-rb install-rb-default
|
244
|
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install-rb-default: pre-install-rb-default
|
245
|
-
pre-install-rb: Makefile
|
246
|
-
pre-install-rb-default: Makefile
|
247
|
-
pre-install-rb-default:
|
248
|
-
@$(NULLCMD)
|
249
|
-
$(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
|
250
|
-
$(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
|
251
|
-
$(Q) $(TOUCH) $@
|
252
|
-
|
253
|
-
site-install: site-install-so site-install-rb
|
254
|
-
site-install-so: install-so
|
255
|
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site-install-rb: install-rb
|
256
|
-
|
257
|
-
.SUFFIXES: .c .m .cc .mm .cxx .cpp .o .S
|
258
|
-
|
259
|
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.cc.o:
|
260
|
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$(ECHO) compiling $(<)
|
261
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
|
262
|
-
|
263
|
-
.cc.S:
|
264
|
-
$(ECHO) translating $(<)
|
265
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
|
266
|
-
|
267
|
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.mm.o:
|
268
|
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$(ECHO) compiling $(<)
|
269
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
|
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|
-
|
271
|
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.mm.S:
|
272
|
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$(ECHO) translating $(<)
|
273
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
|
274
|
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|
275
|
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.cxx.o:
|
276
|
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$(ECHO) compiling $(<)
|
277
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
|
278
|
-
|
279
|
-
.cxx.S:
|
280
|
-
$(ECHO) translating $(<)
|
281
|
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
|
282
|
-
|
283
|
-
.cpp.o:
|
284
|
-
$(ECHO) compiling $(<)
|
285
|
-
$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
|
286
|
-
|
287
|
-
.cpp.S:
|
288
|
-
$(ECHO) translating $(<)
|
289
|
-
$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
|
290
|
-
|
291
|
-
.c.o:
|
292
|
-
$(ECHO) compiling $(<)
|
293
|
-
$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
|
294
|
-
|
295
|
-
.c.S:
|
296
|
-
$(ECHO) translating $(<)
|
297
|
-
$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
|
298
|
-
|
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
|
-
|
data/ext/bioseqalign/extconf.rb~
DELETED
@@ -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
|
-
}
|
data/ext/bioseqalign/runTest.rb
DELETED
@@ -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
|
-
|