| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | hmm.cpp | 198 else return BadScore(); in BranchScore()
236 else return BadScore(); in BranchScore()
303 else return BadScore(); in BranchScore()
332 return BadScore(); in BranchScore()
371 else return BadScore(); in BranchScore()
376 else return BadScore(); in BranchScore()
378 else return BadScore(); in BranchScore()
386 else return BadScore(); in BranchScore()
390 else return BadScore(); in BranchScore()
627 m_lnThrough[i] = (lnthrough == BadScore()) ? BadScore() : m_lnDen[i]+lnthrough; in SetSeqLen()
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| H A D | hmm_inlines.hpp | 88 if(s == BadScore()) return BadScore(); in Score()
109 if(first-order < 0 || last >= (int)seq.size()) return BadScore(); // out of range in Score()
110 if(seq[i+1] != enG || (seq[i+2] != enT && seq[i+2] != enC)) return BadScore(); // no GT/GC in Score()
134 if(first-order < 0 || last >= (int)seq.size()) return BadScore(); // out of range in Score()
135 if(seq[i-1] != enA || seq[i] != enG) return BadScore(); // no AG in Score()
168 if(i-order < 0) return BadScore(); // out of range in Score()
182 if(i-order < 0) return BadScore(); // out of range in Score()
211 if(score == BadScore()) return; in EvaluateInitialScore()
215 if(scr == BadScore()) return; in EvaluateInitialScore()
221 if(scr == BadScore()) return; in EvaluateInitialScore()
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| H A D | score.cpp | 102 … if(strand == ePlus) return (m_dscr[ePlus][i-1] != BadScore()) && (m_ascr[ePlus][j] != BadScore()); in isConsensusIntron()
103 …else return (m_ascr[eMinus][i-1] != BadScore()) && (m_dscr[eMinus][j] != BadScore()… in isConsensusIntron()
845 if(score == BadScore()) score = 0; in Init()
970 if (consensuspenalty != BadScore()) in Init()
1211 if(scr == BadScore()) { in SelectBestReadingFrame()
1226 if(scr == BadScore()) { in SelectBestReadingFrame()
1246 if(scr == BadScore()) { in SelectBestReadingFrame()
1261 if(scr == BadScore()) { in SelectBestReadingFrame()
1285 if(scr == BadScore()) { in SelectBestReadingFrame()
1300 double best_score = BadScore(); in SelectBestReadingFrame()
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| H A D | parse.cpp | 72 rscore = BadScore(); in s_EvaluateNewScore()
84 if(scr == BadScore()) return true; in s_EvaluateNewScore()
89 if(scr == BadScore()) return true; in s_EvaluateNewScore()
99 if(scr == BadScore()) return true; in s_EvaluateNewScore()
103 if(scr == BadScore()) return true; in s_EvaluateNewScore()
109 if(scr == BadScore()) return true; in s_EvaluateNewScore()
126 else if(score == BadScore()) return true; in s_ForwardStep()
141 if(left.Score() != BadScore() && openrgn) in s_ForwardStep()
160 else if(score == BadScore()) return true; in s_ForwardStep()
162 if(left.Score() != BadScore() && openrgn) in s_ForwardStep()
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| H A D | hmm.hpp | 240 if(sc.m_term == BadScore()) sc.m_term = 0; in CalcStateScores()
332 double ThroughLengthScore() const { return BadScore(); } in ThroughLengthScore()
333 double InitialLengthScore() const { return BadScore(); } in InitialLengthScore()
334 double ClosingLengthScore() const { return BadScore(); } in ClosingLengthScore()
360 double BranchScore(const CHMM_State& ) const { return BadScore(); } in BranchScore()
466 return BadScore(); in LengthScore()
473 double BranchScore(const CHMM_State& ) const { return BadScore(); } in BranchScore()
497 if(Strand() != next.Strand()) return BadScore(); in BranchScore()
506 return BadScore(); in BranchScore()
511 if(Strand() != next.Strand()) return BadScore(); in BranchScore()
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| H A D | annot.cpp | 115 ExtendJustThisChain(*it, left, right) == BadScore()) { in TryWithoutObviouslyBadAlignments()
134 return BadScore(); in TryWithoutObviouslyBadAlignments()
140 double score = BadScore(); in TryToEliminateOneAlignment()
151 if (score != BadScore()) { in TryToEliminateOneAlignment()
168 double score = BadScore(); in TryToEliminateAlignmentsFromTail()
232 double score = BadScore(); in Predict()
243 if(score == BadScore()) { in Predict()
251 if(score == BadScore()) { in Predict()
263 if (score == BadScore()) in Predict()
266 if(score == BadScore()) { in Predict()
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| H A D | gnomon_model.cpp | 535 new_cds_info.SetScore( BadScore(), false ); in CombineWith()
587 SetScore( BadScore(), false ); in Clip()
638 SetScore( BadScore(), false ); in Cut()
648 SetScore( BadScore(), false ); in Clear()
710 if (check_start_stop && Score() != BadScore()) { in CdsInvariant()
1473 …SGFFrec() : start(-1), end(-1), score(BadScore()), strand('.'), phase(-1), model(0), tstart(-1), t… in SGFFrec()
1514 if (score == BadScore()) os << dot; else os << score; os << '\t'; in print()
1552 rec.score = v[5]==dot?BadScore():NStr::StringToNumeric<double>(v[5]); in operator >>()
2267 double score = BadScore(); in readGFF3()
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| H A D | gnomon_engine.cpp | 163 mpp, BadScore(), notbridgeable_gaps_len, ggapinfo in Run()
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| H A D | chainer.cpp | 326 CGene() : m_maxscore(BadScore()) {} in CGene()
1918 if(algn.Score() == BadScore()) in InsertMember()
2198 if(algn.Score() != BadScore()) in ScoreCdnas()
2225 if(algn.Score() != BadScore()) { in Duplicate5pendsAndShortCDSes()
2882 return (mp->m_cds_info->Score() != BadScore()); in MemberIsCoding()
3162 if(chain.Score() == BadScore()) in MakeChains()
3918 if(chain.Score() == BadScore()) in CreateChainsForPartialProteins()
4110 return 0.99*BadScore(); in GoodCDNAScore()
6296 if(align.Score() == BadScore()) { in FindSelenoproteinsClipProteinsToStartStop()
6707 …if(itt->Strand() != jtt->Strand() || (itt->Score() != BadScore() && jtt->Score() != BadScore())) c… in FilterOutBadScoreChainsHavingBetterCompatibles()
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| H A D | gnomon_objmgr.cpp | 770 if(*startscore != BadScore()) { in GetScore()
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| H A D | asn1.cpp | 667 if (model.Score() != BadScore()) in create_internal_feature()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon.hpp | 95 …ol rightwall, bool leftanchor, bool rightanchor, double mpp, double consensuspenalty = BadScore(),
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| H A D | gnomon_model.hpp | 63 double BadScore() { return -numeric_limits<double>::max(); } in BadScore() function
225 …confirmed_start(false), m_confirmed_stop(false), m_open(false), m_score(BadScore()), m_genomic_coo… in CCDSInfo()
298 _ASSERT( Score()==BadScore() ); in Invariant()
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| /dports/games/gnuchess/gnuchess-6.2.9/src/engine/ |
| H A D | sort.cpp | 55 static const int BadScore = -28000; variable
704 value += BadScore; in capture_value()
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| /dports/games/scid/scid/engines/togaII1.2.1a/src/ |
| H A D | sort.cpp | 33 static const int BadScore = -28000; variable
801 value += BadScore; in capture_value()
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