本文整理汇总了C++中AlignmentPtr::addLeafGenome方法的典型用法代码示例。如果您正苦于以下问题:C++ AlignmentPtr::addLeafGenome方法的具体用法?C++ AlignmentPtr::addLeafGenome怎么用?C++ AlignmentPtr::addLeafGenome使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类AlignmentPtr
的用法示例。
在下文中一共展示了AlignmentPtr::addLeafGenome方法的4个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: createCallBack
void MappedSegmentMapDupeTest::createCallBack(AlignmentPtr alignment)
{
vector<Sequence::Info> seqVec(1);
BottomSegmentIteratorPtr bi;
BottomSegmentStruct bs;
TopSegmentIteratorPtr ti;
TopSegmentStruct ts;
// setup simple case were there is an edge from a parent to
// child and it is reversed
Genome* parent = alignment->addRootGenome("parent");
Genome* child1 = alignment->addLeafGenome("child1", "parent", 1);
Genome* child2 = alignment->addLeafGenome("child2", "parent", 1);
seqVec[0] = Sequence::Info("Sequence", 3, 0, 1);
parent->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 9, 3, 0);
child1->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 9, 3, 0);
child2->setDimensions(seqVec);
parent->setString("CCC");
child1->setString("CCCTACGTG");
child2->setString("CCCTACGTG");
bi = parent->getBottomSegmentIterator();
bs.set(0, 3);
bs._children.push_back(pair<hal_size_t, bool>(0, true));
bs._children.push_back(pair<hal_size_t, bool>(0, false));
bs.applyTo(bi);
ti = child1->getTopSegmentIterator();
ts.set(0, 3, 0, true, NULL_INDEX, 1);
ts.applyTo(ti);
ti->toRight();
ts.set(3, 3, 0, true, NULL_INDEX, 2);
ts.applyTo(ti);
ti->toRight();
ts.set(6, 3, 0, true, NULL_INDEX, 0);
ts.applyTo(ti);
ti = child2->getTopSegmentIterator();
ts.set(0, 3, 0, false);
ts.applyTo(ti);
ti->toRight();
ts.set(3, 3, NULL_INDEX, true);
ts.applyTo(ti);
ti->toRight();
ts.set(6, 3, NULL_INDEX, false);
ts.applyTo(ti);
}
示例2: createCallBack
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);
}
示例3: createCallBack
void TopSegmentIteratorReverseTest::createCallBack(AlignmentPtr alignment)
{
vector<Sequence::Info> seqVec(1);
BottomSegmentIteratorPtr bi;
BottomSegmentStruct bs;
TopSegmentIteratorPtr ti;
TopSegmentStruct ts;
// setup simple case were there is an edge from a parent to
// child and it is reversed
Genome* parent1 = alignment->addRootGenome("parent1");
Genome* child1 = alignment->addLeafGenome("child1", "parent1", 1);
seqVec[0] = Sequence::Info("Sequence", 10, 2, 2);
parent1->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 10, 2, 2);
child1->setDimensions(seqVec);
parent1->setString("CCCTACGTGC");
child1->setString("CCCTACGTGC");
bi = parent1->getBottomSegmentIterator();
bs.set(0, 10, 0);
bs._children.push_back(pair<hal_size_t, bool>(0, true));
bs.applyTo(bi);
ti = child1->getTopSegmentIterator();
ts.set(0, 10, 0, true, 0);
ts.applyTo(ti);
bi = child1->getBottomSegmentIterator();
bs.set(0, 5, 0);
bs._children.clear();
bs.applyTo(bi);
bi->toRight();
bs.set(5, 5, 0);
bs.applyTo(bi);
}
示例4: main
int main(int argc, char *argv[])
{
CLParserPtr optParser = initParser();
string inPath, botAlignmentPath, topAlignmentPath, parentName, insertName,
childName, leafName;
double upperBranchLength, leafBranchLength;
bool noMarkAncestors;
try {
optParser->parseOptions(argc, argv);
inPath = optParser->getArgument<string>("inFile");
botAlignmentPath = optParser->getArgument<string>("botAlignmentFile");
topAlignmentPath = optParser->getArgument<string>("topAlignmentFile");
parentName = optParser->getArgument<string>("parentName");
insertName = optParser->getArgument<string>("insertName");
childName = optParser->getArgument<string>("childName");
leafName = optParser->getArgument<string>("leafName");
upperBranchLength = optParser->getArgument<double>("upperBranchLength");
leafBranchLength = optParser->getArgument<double>("leafBranchLength");
noMarkAncestors = optParser->getFlag("noMarkAncestors");
} catch (exception &e) {
optParser->printUsage(cerr);
return 1;
}
AlignmentPtr mainAlignment = openHalAlignment(inPath, optParser);
AlignmentConstPtr botAlignment = openHalAlignment(botAlignmentPath,
optParser);
AlignmentConstPtr topAlignment = openHalAlignment(topAlignmentPath,
optParser);
mainAlignment->insertGenome(insertName, parentName, childName,
upperBranchLength);
mainAlignment->addLeafGenome(leafName, insertName, leafBranchLength);
// Insert the new intermediate node.
Genome *insertGenome = mainAlignment->openGenome(insertName);
const Genome *topInsertGenome = topAlignment->openGenome(insertName);
const Genome *botInsertGenome = botAlignment->openGenome(insertName);
topInsertGenome->copyDimensions(insertGenome);
topInsertGenome->copyTopDimensions(insertGenome);
botInsertGenome->copyBottomDimensions(insertGenome);
topInsertGenome->copySequence(insertGenome);
topInsertGenome->copyTopSegments(insertGenome);
topInsertGenome->copyMetadata(insertGenome);
botInsertGenome->copyBottomSegments(insertGenome);
insertGenome->fixParseInfo();
// Copy the bottom segments for the parent genome from the top alignment.
Genome *parentGenome = mainAlignment->openGenome(parentName);
const Genome *botParentGenome = topAlignment->openGenome(parentName);
botParentGenome->copyBottomDimensions(parentGenome);
botParentGenome->copyBottomSegments(parentGenome);
parentGenome->fixParseInfo();
// Fix the parent's other children as well.
vector<string> allChildren = mainAlignment->getChildNames(parentName);
for (size_t i = 0; i < allChildren.size(); i++)
{
if (allChildren[i] != insertName)
{
Genome *outGenome = mainAlignment->openGenome(allChildren[i]);
const Genome *topSegmentsGenome = topAlignment->openGenome(allChildren[i]);
topSegmentsGenome->copyTopDimensions(outGenome);
topSegmentsGenome->copyTopSegments(outGenome);
outGenome->fixParseInfo();
}
}
// Copy the top segments for the child genome from the bottom alignment.
Genome *childGenome = mainAlignment->openGenome(childName);
const Genome *topChildGenome = botAlignment->openGenome(childName);
topChildGenome->copyTopDimensions(childGenome);
topChildGenome->copyTopSegments(childGenome);
childGenome->fixParseInfo();
// Copy the entire genome for the leaf from the bottom alignment.
Genome *outLeafGenome = mainAlignment->openGenome(leafName);
const Genome *inLeafGenome = botAlignment->openGenome(leafName);
inLeafGenome->copy(outLeafGenome);
if (!noMarkAncestors) {
markAncestorsForUpdate(mainAlignment, insertName);
}
mainAlignment->close();
botAlignment->close();
topAlignment->close();
}