pjotrp

# BioRuby to BioScala adapter

require 'java'
require 'bio'

class RbSequence
  def translate(sequence, frame, codon_table)
    seq = Bio::Sequence::NA.new(sequence)
    seq.translate(frame,codon_table)
  end

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import org.scalatest.FlatSpec
import org.scalatest.matchers.ShouldMatchers

package bio.test {

  class BioRubySpec extends FlatSpec with ShouldMatchers {
    import bio.ruby._
    
    "A DNA sequence" should "translate" in {
      val rbseq = new RbSequence

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#! /bin/sh
classpath=.:/usr/share/java/jruby.jar:~/.scala/jruby-complete-1.5.0.RC1.jar

echo "Compile Rubyadapters"
mkdir -p bio/ruby
cd src/bio/ruby
jrubyc --java rbsequence.rb
echo "package bio.ruby;"|cat - RbSequence.java > x.java && mv x.java RbSequence.java
javac -cp $classpath RbSequence.java
mv RbSequence.class ../../../bio/ruby/

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"splitSimplePass1" should "split on dash" in {
  splitSimplePass1("ag--ct-t".toList,Gap1) should equal (List(List('a','g'),List('-','-'),List('c','t'),List('-'),List('t')))
}

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   val Gap1 = '-'
    def splitSimplePass1(seq: List[Char], gap: Char): List[List[Char]] = {
      def isMatch(inGapped: Boolean, c: Char)  = {
        if (inGapped) 
          c == gap
        else
          c != gap
      }
      val isGap = (seq(0) == gap)
      val s = seq.takeWhile{ isMatch(isGap,_) }

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"splitSimplePass2" should "split on Gap2" in {
  splitSimplePass2(List(A,G,Gap2,Gap2,C,T,Gap2,T),Gap2) should equal (List(List(A,G),List(Gap2,Gap2),List(C,T),List(Gap2),List(T)))
}

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case class Symbol()
case object Gap2 extends Symbol
case object A extends Symbol
case object G extends Symbol
case object C extends Symbol
case object T extends Symbol

def splitSimplePass2(seq: List[Symbol], gap: Symbol): List[List[Symbol]] = {
  def isMatch(inGapped: Boolean, c: Symbol) = {
    if (inGapped) 

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  class GapSplitting3Spec extends FlatSpec with ShouldMatchers {
    case class Symbol()
    case object Gap extends Symbol
    case object A extends Symbol
    case object G extends Symbol
    case object C extends Symbol
    case object T extends Symbol
    def splitSimplePass3(seq: List[Symbol]): List[List[Symbol]] = {
      val gap = Gap
      val isGap = (seq(0) == gap)

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    case class Symbol()
    case object Gap extends Symbol
    case class Nucleotide() extends Symbol
    case object GapN extends Nucleotide
    case object A extends Nucleotide
    case object G extends Nucleotide
    case object C extends Nucleotide
    case object T extends Nucleotide
    def splitSimplePass4(seq: List[Symbol]): List[List[Symbol]] = {
      val gap = GapN

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    case class Symbol() {
      def isGap() = false
    }
    case object Gap extends Symbol {
      override def isGap() = true 
    }
    case class Nucleotide() extends Symbol
    case object GapN extends Nucleotide {
      override def isGap() = true 
    }