require_relative 'test_helper'
require 'minitest/autorun'
require 'genevalidator/sequences'
require 'genevalidator/hsp'
module GeneValidator
  class TestSequenceClass < Minitest::Test
    describe 'Test Sequence Class' do

      it 'should get sequence by accession for mrna' do
        seq_mrna = Sequence.new
        seq_mrna.get_sequence_by_accession_no('EF100000', 'nucleotide', 'swissprot -remote')
        assert_equal('AGAGTTTGAT', seq_mrna.raw_sequence[0..9])
        assert_equal('GCCCGTCAAG', seq_mrna.raw_sequence[seq_mrna.raw_sequence.length - 10..seq_mrna.raw_sequence.length - 1])
      end

      it 'should get sequence by accession for protein' do
        seq_prot = Sequence.new
        seq_prot.get_sequence_by_accession_no('F8WCM5', 'protein', 'swissprot -remote')
        assert_equal('MALWMRLLPL', seq_prot.raw_sequence[0..9])
        assert_equal('WPRRPQRSQN', seq_prot.raw_sequence[seq_prot.raw_sequence.length - 10..seq_prot.raw_sequence.length - 1])
      end

      it 'should initialize seq tabular attributes' do
        identifier   = 'sp|Q8N302|AGGF1_HUMAN'
        accession_no = "Q8N302"
        slen         = 714
        seq          = Sequence.new
        hash = {"qseqid"=> "GB10034-PA",
                "sseqid"=> identifier,
                "sacc"=> accession_no,
                "slen"=> slen}

        seq.init_tabular_attribute(hash)

        assert_equal(identifier, seq.identifier)
        assert_equal(accession_no, seq.accession_no)
        assert_equal(slen, seq.length_protein)
        assert(seq.length_protein.is_a? Fixnum)
      end

      it 'should initialize hsp tabular attributes' do
        qseqid = "sp|Q8GBW6|12S_PROFR"
        sseqid = "sp|A5GSN7|ACCD_SYNR3"
        sacc   = "A5GSN7"
        slen   = "291"
        qstart = "49"
        qend   = "217"
        sstart = "65"
        send   = "247"
        length = "183"
        qframe = "1"
        pident = "34.43"
        nident = "63.0"
        evalue = "8.0e-12"
        qseq   = "ERLNNLLDPHSFDEVG---------"
        sseq   = "ERLRILLDPGSFIPVDGELSPTDPL"


        hash = {"qseqid" => qseqid,
                "sseqid" => sseqid,
                "sacc"   => sacc,
                "slen"   => slen,
                "qstart" => qstart,
                "qend"   => qend,
                "sstart" => sstart,
                "send"   => send,
                "length" => length,
                "qframe" => qframe,
                "pident" => pident,
                "nident" => nident,
                "evalue" => evalue,
                "qseq"   => qseq,
                "sseq"   => sseq}

        seq = Hsp.new
        seq.init_tabular_attribute(hash)

        assert_equal(qstart, seq.match_query_from.to_s)
        assert_equal(qend, seq.match_query_to.to_s)
        assert_equal(qframe, seq.query_reading_frame.to_s)
        assert_equal(sstart, seq.hit_from.to_s)
        assert_equal(send, seq.hit_to.to_s)
        assert_equal(qseq, seq.query_alignment.to_s)
        assert_equal(sseq, seq.hit_alignment.to_s)
        assert_equal(length, seq.align_len.to_s)
        assert_equal(pident, seq.pidentity.to_s)
        assert_equal(nident, seq.identity.to_s)
        assert_equal(evalue, seq.hsp_evalue.to_s)

        assert(seq.match_query_from.is_a? Fixnum)
        assert(seq.match_query_to.is_a? Fixnum)
        assert(seq.query_reading_frame.is_a? Fixnum)
        assert(seq.hit_from.is_a? Fixnum)
        assert(seq.hit_to.is_a? Fixnum)
        assert(seq.query_alignment.is_a? String)
        assert(seq.hit_alignment.is_a? String)
        assert(seq.align_len.is_a? Fixnum)
        assert(seq.pidentity.is_a? Float)
        assert(seq.identity.is_a? Float)
        assert(seq.hsp_evalue.is_a? Float)
      end
    end
  end
end