/**
* Add a Gene object reference to locusGenes
*
* @see http://www.doctrine-project.org/api/common/2.5/class-Doctrine.Common.Collections.ArrayCollection.html
* Doctrine documentation on the class ArrayCollection
* @param \bcGen\MainBundle\Entity\Gene $gene
*
* @return Locus
*/
public function addLocusGenes(\bcGen\MainBundle\Entity\Gene $gene)
{
$this->locusGenes[] = $gene;
$gene->setGeneLocus($this);
return $this;
}
/**
* Test the geneAccessionComp() method from the Gene class
*
* @todo Think to a new version of this test
*
* @uses \bcGen\MainBundle\Entity\Gene::geneAccessionComp()
*/
public function testGeneAccessionComp7()
{
echo "\n********************Test GeneAccessionComp7()***********************************************\n";
$result = 0;
$result = \bcGen\MainBundle\Entity\Gene::geneAccessionComp($this->genes[5], $this->genes[1]);
$result += \bcGen\MainBundle\Entity\Gene::geneAccessionComp($this->genes[5], $this->genes[2]);
$result += \bcGen\MainBundle\Entity\Gene::geneAccessionComp($this->genes[5], $this->genes[3]);
$result += \bcGen\MainBundle\Entity\Gene::geneAccessionComp($this->genes[5], $this->genes[4]);
$this->assertEquals(4, $result);
}
/**
*
* {@inheritDoc}
*
* @see \Doctrine\Common\DataFixtures\FixtureInterface::load()
*
* @param Doctrine\Common\Persistence\ObjectManager $manager
*/
public function load(ObjectManager $manager)
{
$gene1 = new Gene();
$gene1->setGeneAccession('GeneAccessionTU1');
$gene1->setGeneContig(1);
$gene1->setGeneRef(TRUE);
$gene1->setGeneSeq('GeneSeqTU1');
$gene1->setGeneGenome($this->getReference('GenomeTU1'));
$gene1->setGeneLocus($this->getReference('LocusTU1'));
$gene1->addGeneAnnotations($this->getReference('AnnotationTU1'));
$gene1->addGeneProteins($this->getReference('ProteinTU1'));
$gene1->addGeneProteins($this->getReference('ProteinTU2'));
$gene1->addGeneProteins($this->getReference('ProteinTU3'));
$gene1->addGeneSources($this->getReference('PublicationTU1'));
$manager->persist($gene1);
$this->addReference('GeneTU1', $gene1);
$gene2 = new Gene();
$gene2->setGeneAccession('GeneAccessionTU2');
$gene2->setGeneContig(2);
$gene2->setGeneRef(FALSE);
$gene2->setGeneSeq('GeneSeqTU2');
$gene2->setGeneGenome($this->getReference('GenomeTU1'));
$gene2->setGeneLocus($this->getReference('LocusTU1'));
$gene2->addGeneAnnotations($this->getReference('AnnotationTU1'));
$gene2->addGeneAnnotations($this->getReference('AnnotationTU2'));
$gene2->addGeneProteins($this->getReference('ProteinTU4'));
$gene2->addGeneProteins($this->getReference('ProteinTU5'));
$gene2->addGeneProteins($this->getReference('ProteinTU6'));
$gene2->addGeneSources($this->getReference('PublicationTU1'));
$manager->persist($gene2);
$this->addReference('GeneTU2', $gene2);
$gene3 = new Gene();
$gene3->setGeneAccession('GeneAccessionTU3');
$gene3->setGeneContig(3);
$gene3->setGeneRef(TRUE);
$gene3->setGeneSeq('GeneSeqTU3');
$gene2->setGeneGenome($this->getReference('GenomeTU1'));
$gene2->setGeneLocus($this->getReference('LocusTU1'));
$gene3->addGeneAnnotations($this->getReference('AnnotationTU2'));
$gene3->addGeneAnnotations($this->getReference('AnnotationTU3'));
$gene3->addGeneProteins($this->getReference('ProteinTU7'));
$gene3->addGeneProteins($this->getReference('ProteinTU8'));
$gene3->addGeneProteins($this->getReference('ProteinTU9'));
$gene3->addGeneSources($this->getReference('PublicationTU1'));
$manager->persist($gene3);
$this->addReference('GeneTU3', $gene3);
$gene4 = new Gene();
$gene4->setGeneAccession('GeneAccessionTU4');
$gene4->setGeneContig(4);
$gene4->setGeneRef(FALSE);
$gene4->setGeneSeq('GeneSeqTU4');
$gene4->setGeneGenome($this->getReference('GenomeTU1'));
$gene4->setGeneLocus($this->getReference('LocusTU1'));
$gene4->addGeneAnnotations($this->getReference('AnnotationTU3'));
$gene4->addGeneProteins($this->getReference('ProteinTU10'));
$gene4->addGeneProteins($this->getReference('ProteinTU11'));
$gene4->addGeneProteins($this->getReference('ProteinTU12'));
$gene4->addGeneSources($this->getReference('PublicationTU1'));
$manager->persist($gene4);
$this->addReference('GeneTU4', $gene4);
$gene5 = new Gene();
$gene5->setGeneAccession('GeneAccessionTU5');
$gene5->setGeneContig(5);
$gene5->setGeneRef(TRUE);
$gene5->setGeneSeq('GeneSeqTU5');
$gene5->setGeneGenome($this->getReference('GenomeTU1'));
$gene5->setGeneLocus($this->getReference('LocusTU1'));
$gene5->addGeneAnnotations($this->getReference('AnnotationTU4'));
$gene5->addGeneProteins($this->getReference('ProteinTU13'));
$gene5->addGeneProteins($this->getReference('ProteinTU14'));
$gene5->addGeneProteins($this->getReference('ProteinTU15'));
$gene5->addGeneSources($this->getReference('PublicationTU1'));
$manager->persist($gene5);
$this->addReference('GeneTU5', $gene5);
$manager->flush();
}
