void subgraph()
{
StringGraph* pGraph = SGUtil::loadASQG(opt::asqgFile, 0, true, opt::maxEdges);
pGraph->printMemSize();
// Remove containments from the graph
SGContainRemoveVisitor containVisit;
std::cout << "Removing contained vertices\n";
while(pGraph->hasContainment())
{
pGraph->visit(containVisit);
}
if (opt::maxOverlap)
{
SGMaximalOverlapVisitor moVisit(-1);
// Remove non-maximal overlap edges
std::cout << "Removing non-maximal overlap edges from graph\n";
pGraph->visit(moVisit);
}
StringGraph* pSubgraph = new StringGraph;
// Set the graph parameters to match the main graph
pSubgraph->setContainmentFlag(pGraph->hasContainment());
pSubgraph->setTransitiveFlag(pGraph->hasTransitive());
pSubgraph->setMinOverlap(pGraph->getMinOverlap());
pSubgraph->setErrorRate(pGraph->getErrorRate());
// Get the root vertex
Vertex* pRootVertex = pGraph->getVertex(opt::rootID);
if(pRootVertex == NULL)
{
std::cout << "Vertex " << opt::rootID << " not found in the graph.\n";
}
else
{
copyVertexToSubgraph(pSubgraph, pRootVertex);
pRootVertex->setColor(GC_BLACK);
// Recursively add neighbors
addNeighborsToSubgraph(pRootVertex, pSubgraph, opt::span);
// Write the subgraph
pSubgraph->writeASQG(opt::outFile);
}
delete pSubgraph;
delete pGraph;
}
StringGraph* SGUtil::loadASQG(const std::string& filename, const unsigned int minOverlap,
bool allowContainments)
{
// Initialize graph
StringGraph* pGraph = new StringGraph;
std::istream* pReader = createReader(filename);
int stage = 0;
int line = 0;
std::string recordLine;
while(getline(*pReader, recordLine))
{
ASQG::RecordType rt = ASQG::getRecordType(recordLine);
switch(rt)
{
case ASQG::RT_HEADER:
{
if(stage != 0)
{
std::cerr << "Error: Unexpected header record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::HeaderRecord headerRecord(recordLine);
const SQG::IntTag& overlapTag = headerRecord.getOverlapTag();
if(overlapTag.isInitialized())
pGraph->setMinOverlap(overlapTag.get());
else
pGraph->setMinOverlap(0);
const SQG::FloatTag& errorRateTag = headerRecord.getErrorRateTag();
if(errorRateTag.isInitialized())
pGraph->setErrorRate(errorRateTag.get());
const SQG::IntTag& containmentTag = headerRecord.getContainmentTag();
if(containmentTag.isInitialized())
pGraph->setContainmentFlag(containmentTag.get());
else
pGraph->setContainmentFlag(true); // conservatively assume containments are present
const SQG::IntTag& transitiveTag = headerRecord.getTransitiveTag();
if(!transitiveTag.isInitialized())
{
std::cerr << "Warning: ASQG does not have transitive tag\n";
pGraph->setTransitiveFlag(true);
}
else
{
pGraph->setTransitiveFlag(transitiveTag.get());
}
break;
}
case ASQG::RT_VERTEX:
{
// progress the stage if we are done the header
if(stage == 0)
stage = 1;
if(stage != 1)
{
std::cerr << "Error: Unexpected vertex record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::VertexRecord vertexRecord(recordLine);
const SQG::IntTag& ssTag = vertexRecord.getSubstringTag();
Vertex* pVertex = new(pGraph->getVertexAllocator()) Vertex(vertexRecord.getID(), vertexRecord.getSeq());
if(ssTag.isInitialized() && ssTag.get() == 1)
{
// Vertex is a substring of some other vertex, mark it as contained
pVertex->setContained(true);
pGraph->setContainmentFlag(true);
}
pGraph->addVertex(pVertex);
break;
}
case ASQG::RT_EDGE:
{
if(stage == 1)
stage = 2;
if(stage != 2)
{
std::cerr << "Error: Unexpected edge record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::EdgeRecord edgeRecord(recordLine);
const Overlap& ovr = edgeRecord.getOverlap();
// Add the edge to the graph
if(ovr.match.getMinOverlapLength() >= (int)minOverlap)
SGAlgorithms::createEdgesFromOverlap(pGraph, ovr, allowContainments);
break;
}
}
++line;
}
// Remove any duplicate edges
SGDuplicateVisitor dupVisit;
pGraph->visit(dupVisit);
SGGraphStatsVisitor statsVisit;
pGraph->visit(statsVisit);
// Remove identical vertices
// This is much cheaper to do than remove via
// SGContainRemove as no remodelling needs to occur
/*
SGIdenticalRemoveVisitor irv;
pGraph->visit(irv);
// Remove substring vertices
while(pGraph->hasContainment())
{
SGContainRemoveVisitor crv;
pGraph->visit(crv);
}
*/
delete pReader;
return pGraph;
}
