bioseqalign 0.0.1 → 0.0.2

data/ext/bioseqalign/fitalgntest.cpp

@@ -13,7 +13,9 @@ extern "C"
 //void Init_FitAlign()
 void Init_SeqAlign()
 {
-  Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class<PairwiseAlign>("PairwiseAlign")
+  Module rb_cModule = define_module("SeqAlign");
+  //Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class<PairwiseAlign>("PairwiseAlign")
+  Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class_under<PairwiseAlign>(rb_cModule,"PairwiseAlign")
     .define_constructor(Constructor<PairwiseAlign>())
     .define_constructor(Constructor<PairwiseAlign,std::string,std::string>())
     //.define_constructor(Constructor<PairwiseAlign,std::string,std::string,int,int,int>())
@@ -25,23 +27,27 @@ void Init_SeqAlign()
     .define_method("setMatchScore", &PairwiseAlign::setMatchScore)
     .define_method("setMismatchScore", &PairwiseAlign::setMismatchScore)
     .define_method("setIndelScore", &PairwiseAlign::setIndelScore);
-  Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
+  //Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
+  Data_Type<FitAlign> rb_cFitAlign = define_class_under<FitAlign,PairwiseAlign>(rb_cModule,"FitAlign")
     .define_constructor(Constructor<FitAlign>())
     .define_constructor(Constructor<FitAlign,std::string,std::string>())
     //.define_constructor(Constructor<FitAlign,std::string,std::string,int,int,int>())
     .define_method("run", &FitAlign::run)
     .define_method("getAlignment", &FitAlign::getAlignment);
-  Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
+  //Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
+  Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class_under<PrefixSuffixAlign,PairwiseAlign>(rb_cModule, "PrefixSuffixAlign")
     .define_constructor(Constructor<PrefixSuffixAlign>())
     .define_constructor(Constructor<PrefixSuffixAlign,std::string,std::string>())
     .define_method("run", &PrefixSuffixAlign::run)
     .define_method("getAlignment", &PrefixSuffixAlign::getAlignment);
-  Data_Type<LocalAlign> rb_cLocalAlign = define_class<LocalAlign,PairwiseAlign>("LocalAlign")
+  //Data_Type<LocalAlign> rb_cLocalAlign = define_class<LocalAlign,PairwiseAlign>("LocalAlign")
+  Data_Type<LocalAlign> rb_cLocalAlign = define_class_under<LocalAlign,PairwiseAlign>(rb_cModule,"LocalAlign")
     .define_constructor(Constructor<LocalAlign>())
     .define_constructor(Constructor<LocalAlign,std::string,std::string>())
     .define_method("run", &LocalAlign::run)
     .define_method("getAlignment", &LocalAlign::getAlignment);
-  Data_Type<GlobalAlign> rb_cGlobalAlign = define_class<GlobalAlign,PairwiseAlign>("GlobalAlign")
+  //Data_Type<GlobalAlign> rb_cGlobalAlign = define_class<GlobalAlign,PairwiseAlign>("GlobalAlign")
+  Data_Type<GlobalAlign> rb_cGlobalAlign = define_class_under<GlobalAlign,PairwiseAlign>(rb_cModule,"GlobalAlign")
     .define_constructor(Constructor<GlobalAlign>())
     .define_constructor(Constructor<GlobalAlign,std::string,std::string>())
     .define_method("run", &GlobalAlign::run)

data/ext/bioseqalign/runTest.rb

@@ -1,5 +1,23 @@
-#require './PairwiseAlign'
-#require './FitAlign'
+require './SeqAlign'
+
+
+module BSA
+  
+  include SeqAlign
+
+end
+
+fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
+fa.run
+puts fa.getAlignScore
+
+#fa = SeqAlign::FitAlign.new("AAAACCCAAA", "CCC")
+#puts fa
+#fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
+
+
+Process.exit(0)
+
 require './SeqAlign'
 
 sa = PairwiseAlign.new("TCGA", "TCGA")

data/lib/bioseqalign.rb

@@ -1,10 +1,13 @@
 require 'bioseqalign/SeqAlign'
 
-class BioSeqAlign
+module BioSeqAlign
+
+  include SeqAlign
+
   #
   # fit seq2 into seq1, returns the score 
   #
-  def self.fitAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.fitAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
     fa = FitAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -28,7 +31,7 @@ class BioSeqAlign
   #
   # seq2: <tt>--------GCTG--------</tt>
   #
-  def self.fitAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.fitAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
     fa = FitAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -40,7 +43,7 @@ class BioSeqAlign
   # prefix-suffix alignment, returns score. Prefix of seq2 aligned with
   # suffix of seq1
   #
-  def self.prefixSuffixAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.prefixSuffixAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = PrefixSuffixAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -66,7 +69,7 @@ class BioSeqAlign
   #
   # seq2: <tt>--------AAAAAACTGATAC</tt>
   #
-  def self.prefixSuffixAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.prefixSuffixAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = PrefixSuffixAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -77,7 +80,7 @@ class BioSeqAlign
   #
   # local alignment of seq1 and seq2, returns score.
   #
-  def self.localAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.localAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = LocalAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -102,7 +105,7 @@ class BioSeqAlign
   #
   # seq2: <tt>GTCGAT</tt>
   #
-  def self.localAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.localAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = LocalAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -113,7 +116,7 @@ class BioSeqAlign
   #
   # global alignment of seq1 and seq2, returns score.
   #
-  def self.globalAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.globalAlignScore(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = GlobalAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -138,7 +141,7 @@ class BioSeqAlign
   #
   # seq2: <tt>AGGGGTCGATTT</tt>
   #
-  def self.globalAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
+  def BioSeqAlign.globalAlignStr(seq1, seq2,  match=1, mismatch=-1, indel=-1)
     fa = GlobalAlign.new(seq1, seq2)
     fa.setMatchScore(match)
     fa.setMismatchScore(mismatch)
@@ -146,6 +149,5 @@ class BioSeqAlign
     fa.run
     fa.getAlignment
   end
-  
-  
+    
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bioseqalign
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-04 00:00:00.000000000 Z
+date: 2014-08-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rice
@@ -62,7 +62,7 @@ files:
 - ext/bioseqalign/fitalgntest.cpp
 - ext/bioseqalign/GlobalAlign.cpp
 - ext/bioseqalign/FitAlign.cpp
-homepage: http://rubygems.org/gems/bioseqalign
+homepage: https://github.com/stefrb/bioseqalign
 licenses:
 - MIT
 post_install_message: