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NCBI C++ ToolKit: include/algo/align/util/align_compare.hpp Source File

{ e_Interval, e_Exon, e_Span, e_Intron, e_Full };

{e_Equiv, e_Overlap, e_OverlapBetter, e_OverlapWorse, e_NoMatch};

CompareGroup(

&o,

strict_only)

;

PopulateBoundariesMap()

;

list< AutoPtr<SAlignment> > BreakOnBoundaries(

)

;

strict =

,

ignore_not_present =

,

vector<string> &quality_scores = vector<string>(),

score_set_as_blacklist =

,

real_score_tolerance = 0,

ext_set_as_blacklist =

,

, m_IgnoreNotPresent(ignore_not_present)

, m_DisambiguitingScores(scores)

, m_QualityScores(quality_scores)

, m_ScoreSet(score_set)

, m_ScoreSetAsBlacklist(score_set_as_blacklist)

, m_RealScoreTolerance(real_score_tolerance)

, m_ExtSetAsBlacklist(ext_set_as_blacklist)

, m_DistributiveScores(distributive_scores)

, m_CountSplitSet1(0)

, m_CountSplitSet2(0)

, m_CountEquivSet1(0)

, m_CountEquivSet2(0)

, m_CountOverlapSet1(0)

, m_CountOverlapSet2(0)

, m_CountEquivGroups(0)

, m_CountOverlapGroups(0)

, m_CountBasesSet1(0)

, m_CountBasesSet2(0)

, m_CountBasesEquivSet1(0)

, m_CountBasesEquivSet2(0)

, m_CountBasesOverlapSet1(0)

, m_CountBasesOverlapSet2(0)

, m_CountBasesOnlySet1(0)

, m_CountBasesOnlySet2(0)

m_NextSet1Group.empty() && m_NextSet2Group.empty() &&

m_Set1.EndOfData() && m_Set2.EndOfData();

PopulateBoundariesMap();

vector<const SAlignment *> NextGroup();

x_DetermineNextGroupSet();

x_GetCurrentGroup(

);

x_SplitOnOverlaps(

group,

);

size_t CountBasesEquivSet2() const

size_t CountEquivSet1() const

size_t CountOverlapSet1() const

size_t m_CountOverlapGroups

size_t CountOverlapSet2() const

size_t CountBasesOverlapSet2() const

map< string, double > TRealScoreSet

map< TSeqRange, TSeqRange > TAlignmentSpans

list< AutoPtr< SAlignment > > m_NextSet2Group

list< AutoPtr< SAlignment > > m_NextSet1Group

size_t CountSplitSet1() const

size_t m_CountBasesOverlapSet2

size_t CountOnlySet2() const

list< AutoPtr< SAlignment > > m_CurrentSet2Group

size_t m_CountBasesOnlySet2

pair< vector< string >, vector< string > > TDisambiguatingScoreList

size_t m_CountBasesEquivSet1

size_t CountBasesOverlapSet1() const

map< CSeq_id_Handle, set< TSeqPos > > m_BoundariesMap

size_t CountOnlySet1() const

size_t CountEquivSet2() const

size_t m_CountBasesEquivSet2

size_t m_CountOverlapSet1

size_t CountEquivGroups() const

double m_RealScoreTolerance

size_t CountBasesOnlySet2() const

size_t CountBasesOnlySet1() const

bool m_ScoreSetAsBlacklist

size_t CountBasesSet1() const

TDisambiguatingScoreList m_DisambiguitingScores

CAlignCompare(IAlignSource &set1, IAlignSource &set2, EMode mode=e_Interval, bool strict=false, bool ignore_not_present=false, ERowComparison row=e_Both, const TDisambiguatingScoreList &scores=TDisambiguatingScoreList(), const vector< string > &quality_scores=vector< string >(), const set< string > &score_set=set< string >(), bool score_set_as_blacklist=false, double real_score_tolerance=0, const set< string > &ext_set=set< string >(), bool ext_set_as_blacklist=false, const set< string > distributive_scores=set< string >())

size_t CountBasesEquivSet1() const

size_t m_CountBasesOverlapSet1

size_t CountOverlapGroups() const

list< AutoPtr< SAlignment > > m_CurrentSet1Group

pair< vector< int >, vector< int > > TDisambiguatingScoreValues

Optional list of disambiguiting scores; alignments can only be compared if they are equal in these sc...

size_t m_CountBasesOnlySet1

vector< string > m_QualityScores

set< string > m_DistributiveScores

size_t m_CountEquivGroups

map< string, CRef< CUser_object > > TExtSet

size_t CountSplitSet2() const

size_t m_CountOverlapSet2

size_t CountBasesSet2() const

map< string, int > TIntegerScoreSet

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALGOALIGN_EXPORT

ENa_strand

strand of nucleic acid

#define row(bind, expected)

TDisambiguatingScoreValues scores

vector< const SAlignment * > matched_alignments

TRealScoreSet real_scores

vector< double > quality_scores

CAlignCompare & compare_object

ENa_strand subject_strand

TIntegerScoreSet integer_scores

CRangeCollection< TSeqPos > query_mismatches

CRangeCollection< TSeqPos > subject_mismatches

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