void GenomeMetaTest::createCallBack(AlignmentPtr alignment)
{
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome* ancGenome = alignment->addRootGenome("AncGenome", 0);
MetaData* ancMeta = ancGenome->getMetaData();
ancMeta->set("Young", "Jeezy");
}
void GenomeStringTest::createCallBack(AlignmentPtr alignment)
{
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
hal_size_t seqLength = 28889943;
Genome* ancGenome = alignment->addRootGenome("AncGenome", 0);
vector<Sequence::Info> seqVec(1);
seqVec[0] = Sequence::Info("Sequence", seqLength, 5000, 700000);
ancGenome->setDimensions(seqVec);
_string = randomString(seqLength);
ancGenome->setString(_string);
}
void GenomeUpdateTest::createCallBack(AlignmentPtr alignment)
{
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome* ancGenome = alignment->addRootGenome("AncGenome", 0);
vector<Sequence::Info> seqVec(1);
seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 700000);
ancGenome->setDimensions(seqVec);
alignment->close();
alignment->open(_createPath, false);
ancGenome = alignment->openGenome("AncGenome");
seqVec[0] = Sequence::Info("Sequence", 10000005, 14000, 2000001);
ancGenome->setDimensions(seqVec);
}
void GenomeCreateTest::createCallBack(AlignmentPtr alignment)
{
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome* ancGenome = alignment->addRootGenome("AncGenome", 0);
Genome* leaf1Genome = alignment->addLeafGenome("Leaf1", "AncGenome", 0.1);
Genome* leaf2Genome = alignment->addLeafGenome("Leaf2", "AncGenome", 0.2);
Genome* leaf3Genome = alignment->addLeafGenome("Leaf3", "AncGenome", 0.3);
MetaData* ancMeta = ancGenome->getMetaData();
ancMeta->set("Young", "Jeezy");
vector<Sequence::Info> seqVec(1);
seqVec[0] =Sequence::Info("Sequence", 1000000, 5000, 700000);
ancGenome->setDimensions(seqVec);
seqVec[0] =Sequence::Info("Sequence", 1000000, 700000, 0);
leaf1Genome->setDimensions(seqVec);
seqVec[0] =Sequence::Info("Sequence", 2000000, 700000, 0);
leaf2Genome->setDimensions(seqVec);
seqVec[0] =Sequence::Info("Sequence", 3000000, 700000, 0);
leaf3Genome->setDimensions(seqVec);
}