require 'spec_helper'
require 'genomer-plugin-summary/metrics'

describe GenomerPluginSummary::Metrics do

  let(:metric) do
   o = Object.new
   o.extend described_class
   o
  end

  describe "#gc_content" do

    subject do
      metric.gc_content entry_type, scaffold
    end

    context "an empty scaffold" do
      let(:scaffold){ [] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should be_nan }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == be_nan }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == be_nan }
      end

    end

    context "a single contig scaffold" do
      let(:scaffold){ [sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 50.0 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should be_nan }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 50.0 }
      end

    end

    context "a mixed scaffold" do
      let(:scaffold){ [sequence('ATGC'),unresolved('NNNN'),sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 50.0 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == be_nan }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 50.0 }
      end

    end

  end

  describe "#count" do

    subject do
      metric.count entry_type, scaffold
    end

    context "an empty scaffold" do
      let(:scaffold){ [] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 0 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 0 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 0 }
      end

    end

    context "a single contig scaffold" do
      let(:scaffold){ [sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 1 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 0 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 1 }
      end

    end

    context "a mixed scaffold" do
      let(:scaffold){ [sequence('ATGC'),unresolved('NNNN'),sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 2 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 1 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 3 }
      end

    end

  end

  describe "#length" do

    subject do
      metric.length entry_type, scaffold
    end

    context "an empty scaffold" do
      let(:scaffold){ [] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 0 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 0 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 0 }
      end

    end

    context "a single contig scaffold" do
      let(:scaffold){ [sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 4 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 0 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 4 }
      end
    end

    context "a mixed scaffold" do
      let(:scaffold){ [sequence('ATGC'),unresolved('NNNN'),sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 8 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 4 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 12 }
      end
    end

  end

  describe "#percent" do

    subject do
      metric.percent entry_type, scaffold
    end

    context "an empty scaffold" do
      let(:scaffold){ [] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should be_nan }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == be_nan }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == be_nan }
      end

    end

    context "a single contig scaffold" do
      let(:scaffold){ [sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 100.0 }
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 0.0 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 100.0 }
      end
    end

    context "a mixed scaffold" do
      let(:scaffold){ [sequence('ATGC'),unresolved('NNNN'),sequence('ATGC')] }

      context "contigs" do
        let(:entry_type){ :sequence }
        it{ should == 8 / 12.0 * 100}
      end
      context "gaps" do
        let(:entry_type){ :unresolved }
        it{ should == 4 / 12.0 * 100 }
      end
      context "everything" do
        let(:entry_type){ :all }
        it{ should == 100.0 }
      end
    end

  end

  describe "#sequence_total" do

    def row(name,start,stop,percent,gc)
      {:id       => name,
        :type     => :sequence,
        :start    => start,
        :stop     => stop,
        :size     => (stop - start) + 1,
        :percent  => percent,
        :gc       => gc}
    end

    subject do
      metric.sequence_total(sequences)
    end

    context "passed an empty array" do
      let(:sequences) do
        []
      end

      it do
        should == {
          :start   => 0,
          :stop    => 0,
          :size    => 0,
          :percent => 0,
          :gc      => 0 }
      end
    end

    context "passed one entry" do
      let(:sequences) do
        [row('contig1',1,6,100.0,50.0)]
      end

      it do
        should == {
          :start   => 1,
          :stop    => 6,
          :size    => 6,
          :percent => 100.0,
          :gc      => 50.0 }
      end
    end

    context "passed two entries less than 100% of the scaffold" do
      let(:sequences) do
        [row('contig1', 1,  6,  30.0, 50.0),
         row('contig2', 15, 20, 30.0, 50.0)]
      end

      it do
        should == {
          :start   => 1,
          :stop    => 20,
          :size    => 12,
          :percent => 60.0,
          :gc      => 50.0 }
      end
    end
  end

end