Пример #1
0
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");
}
Пример #2
0
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);
}
Пример #3
0
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);  
}
Пример #4
0
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);
}