/** * 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(); }