src/AlignmentTree.cpp File Reference

#include "PhyloTree.h"
#include <sstream>
#include <stack>

Include dependency graph for AlignmentTree.cpp:

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Typedefs
typedef unsigned	uint

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Typedef Documentation

typedef unsigned uint

Definition at line 10 of file AlignmentTree.cpp. Referenced by TreeIntervalMap::add(), analyzeVariableSegments(), BbSeqComp::BbSeqComp(), classifyCoordinateRanges(), classifyIntergenic(), CompactMatchRecord::CompactMatchRecord(), CompactUngappedMatchRecord::CompactUngappedMatchRecord(), compareAlignmentsAceD(), constructCoordList(), detectBackboneBreakOnGenes(), doAlignment(), UniqueMatchFinder::EnumerateMatches(), extractSubAlignment(), featureIntersect(), featureNearestNeighbors(), GappedMatchRecord::finalize(), VectorIntervalMap::find(), TreeIntervalMap::find(), findVariableSegmentsWithFlankingBB(), getAlphabetID(), getBpList(), getLocalRecordHeights(), SeedMatchEnumerator::HashMatch(), IntervalSeqManipulator::IntervalSeqManipulator(), livComp::livComp(), main(), makeAllPairwiseGenomeHSSBreakOnGenes(), makeVariableSegmentsCoordinateList(), MatchRecord::MatchRecord(), neighborhoodListLookup(), operator<<(), processNovelSubsetMatches(), ReadAluFile(), relabelTaxaToStartWithZero(), rerootTree(), setTaxonNames(), and UngappedMatchRecord::UngappedMatchRecord().

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