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Searched refs:TIVec (Results 1 – 9 of 9) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_seq.hpp101 void FindAllStarts(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRa…
102 void FindAllStops(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRan…
104 TIVec starts[3], TIVec stops[3], int& frame, bool obeystart);
H A Dscore.hpp109 TIVec m_laststop[2][3], m_notinexon[2][3], m_notinintron[2], m_notining;
112 TIVec m_asplit[2][2], m_dsplit[2][2];
113 TIVec m_inalign;
114 TIVec m_protnum;
H A Dscore.cpp722 TIVec& nin = m_notinintron[strand]; in Init()
727 TIVec& nex = m_notinexon[strand][frame]; in Init()
880 TIVec& lstp = m_laststop[strand][frame]; in Init()
1187 …odel& model, const CEResidueVec& mrna, const CAlignMap& mrnamap, TIVec starts[3], TIVec stops[3],… in SelectBestReadingFrame()
1317 … TIVec::iterator it_a = lower_bound(starts[frame].begin(),starts[frame].end(),prev_stop+3); in SelectBestReadingFrame()
1320 TIVec::iterator it_b = it_a+1; in SelectBestReadingFrame()
1327 …for(TIVec::iterator it = it_a; it != it_b; it++) { // if extend5p==true this loop incl… in SelectBestReadingFrame()
1398 TIVec starts[3], stops[3]; in GetScore()
1409 ERASE_ITERATE(TIVec, pstp, stops[fr]) { in GetScore()
1474 ITERATE(TIVec, it, starts[fr]) { in GetScore()
H A Dgnomon_seq.cpp147 void FindAllCodonInstances(TIVec positions[], const EResidue codon[], const CEResidueVec& mrna, TSi… in FindAllCodonInstances()
157 void FindAllStarts(TIVec starts[], const CEResidueVec& mrna, TSignedSeqRange search_region, int fix… in FindAllStarts()
162 void FindAllStops(TIVec stops[], const CEResidueVec& mrna, TSignedSeqRange search_region, int fixed… in FindAllStops()
182 … contig_seq, const CEResidueVec& mrna, const CAlignMap& mrnamap, TIVec starts[3], TIVec stops[3],… in FindStartsStops()
H A Daligncollapser.cpp734 TIVec exons_to_align; in CleanSelfTranscript()
765 TIVec score(tseq.size()); in CleanSelfTranscript()
1213 …TIVec left_plus(len,right_end); // closest left + strand splice 'on the right' from the curr… in FilterAlignments()
1214 …TIVec left_minus(len,right_end); // closest left - strand splice 'on the right' from the curr… in FilterAlignments()
1215 …TIVec right_plus(len,m_left_end); // closest right + strand splice 'on the left' from the cu… in FilterAlignments()
1216 …TIVec right_minus(len,m_left_end); // closest right - strand splice 'on the left' from the cu… in FilterAlignments()
1400 TIVec self_coverage(len,0); in FilterAlignments()
1667 TIVec* rights = 0; in FilterAlignments()
1739 TIVec* lefts = 0; in FilterAlignments()
H A Dchainer.cpp318 TIVec m_cap_peaks;
319 TIVec m_polya_peaks;
533 TIVec acds_map(amap.FShiftedLen(a.GetCdsInfo().Cds()),0); in IsAlternative()
548 TIVec cds_map(gmap.FShiftedLen((*it)->GetCdsInfo().Cds()),0); in IsAlternative()
2651 TIVec right_ends(pointers.size()); in LeftRight()
2667 …TIVec::iterator lb = lower_bound(right_ends.begin(),right_ends.end(),ai.Limits().GetFrom()-2*flex_… in LeftRight()
2710 TIVec left_ends(pointers.size()); in RightLeft()
3480 TIVec right_ends(pointers.size()); in FindOptimalChainForProtein()
5238 TIVec peaks(3, -1); in MainPeaks()
7916 TIVec exons(length,0); in SetGenomic()
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H A Dannot.cpp209 TIVec busy_spots(rlimit+1,0); in Predict()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon.hpp90 …TIVec starts[3], TIVec stops[3], int& frame, int& best_start, int& best_stop, bool extend5p = tru…
H A Dgnomon_model.hpp72 typedef vector<int> TIVec; typedef