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seq.hpp
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// seq.hpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Sequence utilities
*
*/
#ifndef SEQ_HPP
#define SEQ_HPP
#include "common.hpp"
using namespace Common_sp;
namespace Seq_sp
{
// Frame
typedef char Frame;
// -3, -2, -1, 1, 2, 3
// If > 0 then strand = 1 else strand = -1
inline bool isFrame (char frame)
{ return
betweenEqual (frame, char (-3), char (-1)) ||
betweenEqual (frame, char ( 1), char ( 3));
}
// Strand
typedef char Strand;
// 1 - top
// -1 - bottom
// 0 - unknown
inline bool isStrand (char strand)
{ return strand == -1
|| strand == 1;
}
// Alphabets
// DNA
// Lower case: gap is impossible
// Upper case: gap is possible
extern const char* dnaAlphabet;
// Nucleotides:
// 'a' - adenine
// 'c' - cytosine
// 'g' - guanine
// 't' - thymine (RNA: 'u' - uracil)
extern const char* dnaWildcards;
/*
IUPAC:
m = ac
r = ag (purins)
w = at
s = cg
y = ct (pyramidins)
k = gt (ketons)
v = acg
h = act
d = agt
b = cgt
n = acgt
*/
inline bool isAmbigNucl (char c)
{ return strchr (dnaWildcards, c); }
extern const char* extDnaAlphabet;
// = DnaAlphabet + DnaWildcards
extern const char* extSparseDnaAlphabet;
// extDnaAlphabet + gap
// '-': gap
// ' ': nothing
// Peptides
// Lower case
extern const char* peptideAlphabet;
// Amino acides
extern const char* peptideWildcards;
inline bool isAmbigAa (char c)
{ return strchr (peptideWildcards, c); }
extern const char* extPeptideAlphabet;
// = PeptideAlphabet + PeptideWildcards
/*
X = any
B = DN
Z = EQ
J = IL
U = selenocysteine ("tga")
O = Pyrrolysine ("tag")
*/
extern const char* terminator;
// strlen() = 1
extern const char* extTermPeptideAlphabet;
// = ExtPeptideAlphabet + terminator
extern const char* extSparseTermPeptideAlphabet;
// = extPeptideAlphabet + gap
size_t alphabet2Pos (const char* alphabet,
char c);
// Return: position of c in alphabet[]
// Requires: c in alphabet[]
inline bool isAmbig (char c,
bool aa)
{ return aa ? isAmbigAa (c) : isAmbigNucl (c); }
typedef unsigned char Gencode;
// NCBI genetic code
/////////////////////////// Seq //////////////////////////////////
// "Sparse sequence" is a sequence with '-'
inline size_t countInsertions (const string &seq)
{ return strCountSet (seq, "-"); }
inline size_t sparseSeqLen (const string &seq)
{ return seq. size () - countInsertions (seq); }
#if 0
int SparseSeq2SeqPos (const char* SparseSeq,
int SparseSeqPos);
int Seq2SparseSeqPos (const char* SparseSeq,
int SeqPos);
// Return: SparseSeq [Result] != '-'
#endif
extern const size_t fastaLineLen;
typedef char (*GetIintersectChar) (const char* CharSet);
// Input: CharSet[]
// Return: Intersection character, ' ' if no intersection
struct Dna;
struct Peptide;
struct Seq : Named
// name: name of sequence
// Positions: 0-based
// stop: position of the last character + 1
// start != pos
// size = stop - start
// Reverse strand <=> start > stop
{
string seq;
// in getSeqAlphabet()
// May be empty()
bool sparse {false};
// true <=> '-' is allowed
protected:
Seq () = default;
Seq (const string &name_arg,
size_t seqLen,
bool sparse_arg)
: Named (name_arg)
, seq (seqLen, '\0')
, sparse (sparse_arg)
{ qcName (); }
Seq (const string &name_arg,
const string &seq_arg,
bool sparse_arg)
: Named (name_arg)
, seq (seq_arg)
, sparse (sparse_arg)
{ qcName ();
if (! sparse)
unSparse ();
}
Seq (LineInput &fasta,
size_t reserveLen,
bool sparse_arg,
bool makeUpper);
// Reads 1 sequence and skips blank lines
// Requires: fasta.line is the first line of the sequence
// If !makeUpper then make lowercase
void qcName () const;
void qcAlphabet () const;
// Invokes: getSeqAlphabet()
static LineInput* getLineInput (const string &fName)
{ LineInput* in = new LineInput (fName);
in->nextLine ();
return in;
}
public:
virtual Seq* copy () const override = 0;
void qc () const override
{ if (! qc_on)
return;
qcName ();
qcAlphabet ();
}
virtual const Dna* asDna () const
{ return nullptr; }
virtual const Peptide* asPeptide () const
{ return nullptr; }
virtual const char* getSeqAlphabet () const = 0;
virtual bool isAmbiguous (char c) const = 0;
void printCase (ostream &os,
bool makeUpper) const;
// FASTA format
// Length of lines = fastaLineLen
size_t getIdSize () const
{ const size_t idSize = name. find (' ');
return idSize == string::npos ? name. size () : idSize;
}
static size_t getTaxonStart (const string &s);
// Return: != string::npos => s[Return] == '['
size_t getTaxonStart () const
{ return getTaxonStart (name); }
string getId () const
{ return name. substr (0, getIdSize ()); }
long /*CSeq_id::TGi*/ getGi () const;
// If there is no gi then throw
string getDescription (bool trimTaxon) const;
// Return: between Id and taxon
size_t getXs () const;
// Invokes: isAmbiguous()
size_t getContiguousXs () const;
// Return: max. length of contiguous ambiguous characters
virtual double getComplexityInt (size_t start,
size_t end) const = 0;
// Input: Subsequence form start to end
// Return: Entropy of diletters divided by log_2 e; >= 0
// If > stdMinComplexity then no repeats
double getComplexity () const
{ return getComplexityInt (0, seq. size ()); }
#if 0
size_t* GetAlphabetCount () const;
// Return: length = strlen (SeqAlphabet)
// Invokes: NewUintArray ()
#endif
void unSparse ()
{ strDeleteSet (seq, "-");
sparse = false;
}
map<char,size_t> getCharCount () const;
};
struct Multifasta final : Root
/* Usage:
{ Multifasta fa (...);
while (fa. next ())
{Peptide|Dna} ... (fa);
} // To close LineInput and Progress
*/
{
LineInput in;
const bool aa;
Progress prog;
Multifasta (const string &fName,
bool aa_arg,
size_t displayPeriod = 1000)
: in (fName)
, aa (aa_arg)
, prog (0, displayPeriod)
{ in. nextLine ();
qcNewSeq ();
}
private:
void qcNewSeq () const;
public:
bool next () const
{ qcNewSeq ();
return ! in. eof;
}
};
////////////////////////////// Dna /////////////////////////////////
// acgtb: 4 nucleotides and blank
// Blank is encoded by '-'
// One of them must be true
size_t nuc2num (char wildNucleotide);
// Return: if wildNucleotide is in dnaAlphabet then position in dnaAlphabet
// else if wildNucleotide is in dnaWildcards then 4
// else error
// Case-insensitive
#if 0
typedef PROBABILITY NT_PROBABILITY [5];
void PrintNTProb (const NT_PROBABILITY Prob);
void CompressDna (const char* seq,
char* CompressedSeq,
size_t &CompressedSeqLen);
// Input: seq in extDnaAlphabet + '-' + uppercase
// Output: CompressedSeq []
// CompressedSeqLen
// Requires: CompressedSeq [] must have enough space (<= strlen (seq) + 1)
void UncompressDna (size_t SeqLen,
const char* CompressedSeq,
char* &seq,
size_t &CompressedSeqLen);
// Output: *seq, malloc (), length = SeqLen + 1
// CompressedSeqLen
#endif
uchar wild2nucleotides (char wildNucleotide,
bool acgtb [5]);
// Output: acgtb []
// Return: Number of 1's in acgtb []; 0..5
// |WildNucleotide|, "Degree of ambiguity"
// Requires: WildNucleotide in extDnaAlphabet + '-' + ' '
char nucleotides2wild (const bool acgtb [5]);
// Return: in extDnaAlphabet + '-'; if empty set then ' '
#if 0
void Wild2NucleotideFreq (char WildNucleotide,
NT_PROBABILITY acgtb);
// Output: acgtb []
// Sum_i acgtb [i] = 1
#endif
char complementaryNucleotide (char wildNucleotide);
// Return: in extDnaAlphabet
// Possible blank is preserved
// Requires: wildNucleotide in extDnaAlphabet
char getUnionNucleotide (const string &charSet);
// Return: in extDnaAlphabet + '-'; if empty set then ' '
// Requires: CharSet is in extDnaAlphabet + '-'
char getIntersectNucleotide (const string &charSet);
// Return: in extDnaAlphabet + '-'; if empty set then ' '
// Requires: CharSet is in extDnaAlphabet + '-'
bool nucleotideMatch (char wildNucleotide1,
char wildNucleotide2);
// Return: true if the nucleotides of wildNucleotide1 and wildNucleotide2 intersect
#if 0
bool NucleotideSeqMatch (const char* Seq1,
const char* Seq2);
// Requires: Seq1|2 [] - in extDnaAlphabet
bool MoreGeneralNucleotide (char WildNucleotide1,
char WildNucleotide2);
// Return: true if the nucleotides of WildNucleotide1 are a superset
// of those of WildNucleotide2 (i.e., WildNucleotide1 is
// more general than or equal to WildNucleotide2)
void SelectSpecificNucleotides (char* CharSet);
// Delete more general nucleotides
// Update: CharSet []
// Requires: CharSet is in extDnaAlphabet + '-'
size_t CountAmbiguousNucleotides (const char* seq);
// Input: seq - sparse sequence
char* getReverseDna (const char* Source);
// Return: malloc ()
// Requires: source is in extDnaAlphabet + '-'
#endif
string& reverseDna (string &seq);
// Requires: seq is in extDnaAlphabet + '-'
char codon2aa (const char codon [3],
Gencode gencode,
bool lowercasePossibleStartCodon);
// Return: in extTermPeptideAlphabet; lowercasePossibleStartcodon => lower-case
// Requires: codon[] is in extDnaAlphabet
inline size_t dna2codons_len (size_t dna_len)
{ return dna_len ? (dna_len - 1) / 3 + 1 : 0; }
#if 0
inline bool CodonMatch (const char Codon1 [3],
const char Codon2 [3])
{ return NucleotideSeqMatch (Codon1, Codon2); }
// Requires: Codon1|2 [] - in extDnaAlphabet
inline bool TerminatorCodon (const char Codon [3])
{ return Codon2AA (Codon) == '*'; }
bool MayBeTerminatorCodon (const char Codon [3]);
size_t Dna2PeptidePos (size_t DnaPos,
Frame frame,
size_t DnaLen);
size_t Peptide2DnaPos (size_t PeptidePos,
Frame frame,
size_t DnaLen);
#endif
struct Dna : Seq
{
static constexpr double stdMinComplexity {2.0}; // PAR
Dna () = default;
Dna (const string &name_arg,
size_t seqLen,
bool sparse_arg)
: Seq (name_arg, seqLen, sparse_arg)
{}
Dna (const string &name_arg,
const string &seq_arg,
bool sparse_arg)
: Seq (name_arg, seq_arg, sparse_arg)
{}
Dna (LineInput &fasta,
size_t reserveLen,
bool sparse_arg)
: Seq (fasta, reserveLen, sparse_arg, false)
{}
Dna (Multifasta &fasta,
size_t reserveLen,
bool sparse_arg);
Dna* copy () const final
{ return new Dna (*this); }
void saveText (ostream& os) const override
{ printCase (os, false); }
const Dna* asDna () const final
{ return this; }
const char* getSeqAlphabet () const final
{ return sparse ? extSparseDnaAlphabet : extDnaAlphabet; }
bool isAmbiguous (char c) const final
{ return ! strchr (dnaAlphabet, c); }
double getComplexityInt (size_t start,
size_t end) const final;
#if 0
void PrintHTML (bool UpperCase,
PHRED_SCORE MinGoodQual) const;
SEQ_ANNOT_LIST* GetAnnotList (int GoodStart = 0) const;
// List: "seq", "Score 10", "Score 1"
// Qual
void CreateQual ();
// Requires: Qual == nullptr
// Postcondition: Qual != nullptr
bool GoodQual () const;
// Return: false if there are wrong values in Qual []
void CopyQual (const PHRED_SCORE* SourceQual);
// Invokes: CreateQual (), GoodQual ()
void ReadQual (const char* FName);
// Input: FName: FASTA-file with phred quality scores
// Output: Qual
// Invokes: CreateQual (), GoodQual ()
// Requires: Qual != nullptr
void SetQual (PHRED_SCORE DefaultScore);
PHRED_SCORE GetMinQual () const;
PHRED_SCORE GetMaxQual () const;
void Qual2MeanVar (size_t Start,
size_t End,
double &Mean,
double &Var) const;
// Output: Mean, Var (unbiased)
void Qual2N (PHRED_SCORE MinQual,
bool GapCoded);
// If Qual [i] < MinQual then seq [i] := 'N'|'n'
// Delete Qual
void MinScore2Pos (PHRED_SCORE MinScore,
size_t &Start,
size_t &End) const;
// Output: Start, End; valid if Start < End
void QualSaveFile (FILE* F,
PHRED_SCORE DefaultScore) const;
char* Qual2String () const;
// Return: new [], May be nullptr
void DeleteStart (size_t NewStart);
#endif
Dna* makeComplementary () const;
// Return: Reverse and complementary Dna; !nullptr
void reverse ();
// Invokes: makeComplementary ()
Peptide makePeptide (Frame frame,
Gencode gencode,
bool lowercaseStartcodon,
bool firstStartCodon2M,
size_t &translationStart) const;
// Output: translationStart
// Requires: firstStartCodon2M => lowercaseStartcodon
Peptide cds2prot (Gencode gencode,
bool trunc5,
bool trunc3,
bool hasStopCodon,
bool allowExtraStopCodon) const;
// Return: if !trunc3 && hasStopCodon then no '*'
// Invokes: makePeptide(1,gencode,true,true)
Vector<Peptide> getOrfs (Frame frame,
Gencode gencode,
size_t len_min) const;
// Input: len_min: min. Peptide length without 'X'
// Return: Peptide: from '*' to '*'
#if 0
bool ExistsPeptide () const;
// Return: true if there is peptide w/o an internal stop codon in some frame
bool LongestCompleteCDS (size_t MinProteinLen,
size_t &Start,
size_t &End) const;
// Output: Start, End - position after last nt;
// (End - Start) % 3 = 0
// End <= strlen (seq)
// Valid if true
// Return: true if found
void RefineSparse (char* Target,
byte* TargetQual) const;
// Target[]='n' or seq[] is ambiguous
// Update: Target []: sparse sequence
// Qual []; if Target [i] = '-' then TargetQual [i] = 0
bool ContainsAmbiguity () const;
size_t GetAmbiguousPrefixEnd () const;
// = length of ambiguous nt prefix
size_t GetAmbiguousSuffixStart () const;
bool DeleteAmbiguousPrefix ();
// Return: True if non-empty prefix is deleted
bool DeleteAmbiguousSuffix ();
// Return: True if non-empty suffix is trimmed
void TrimN (bool GapCoded);
size_t TrimBadStart (size_t WindowLen,
PROBABILITY MaxAmbigFraction) const;
// Return: Good sequence start
size_t TrimBadEnd (size_t WindowLen,
PROBABILITY MaxAmbigFraction) const;
// Return: Good sequence end
size_t TrimLowComplexityStart () const;
// Return: Good sequence start
size_t TrimLowComplexityEnd () const;
// Return: Good sequence end
#endif
// Poly-nucleotide segment at the end of seq[]
bool polyNucWindow (size_t start,
size_t windowLen,
char nucleotide) const;
// Return: true if most of the nucleotides in the window are nucleotide
size_t findPolyNucEnd (size_t windowLen,
char nucleotide) const;
// Find poly-nucleotide segment at the end of seq
// Return: start of the poly-nucleotide segment; seq.size() if not found
// Invokes: polyNucWindow ()
// PolyA
bool polyAWindow (size_t start,
size_t windowLen) const
{ return polyNucWindow (start, windowLen, 'a'); }
size_t findPolyA (size_t windowLen) const
{ return findPolyNucEnd (windowLen, 'a'); }
size_t removePolyA (size_t windowLen)
{ const size_t polyA_start = findPolyA (windowLen);
const size_t polyA_len = seq. size () - polyA_start;
seq. erase (polyA_start);
return polyA_len;
}
// Non-idempotent
#if 0
// PolyA inside seq[]
void FindPolyAWindow (int &BestStart,
int &BestEnd,
double &MaxWeight) const;
// Output: BestStart = -1 iff MaxWeight < 0
bool DiNucLowComplexity (int &BestStart,
int &BestEnd,
double &MaxWeight,
int &MaxMonoNucLen) const;
// Find a low-complexity segement by di-nucleotide statistics
// Output: Valid if true
// MaxWeight: >= 20: significant
// MaxMonoNucLen: inside [BestStart, BestEnd]
// Return: true if found, MaxWeight >= 0
size_t NucleotideFreq (NT_PROBABILITY acgtb,
size_t Start,
size_t End,
uint Step) const;
// Return: number of nucleotides couned
// Output: acgtb []; sum = 1
size_t NucleotidePairFreq (PROBABILITY acgtb [5] [5]) const;
// Input: Start, End -??
// Return: strlen (seq)
// Output: acgtb [] []; sum = 1
double GetMeltTemp (double DnaConc = 300.0,
double SaltConc = 50.0,
double MgConc = 1.5) const;
// Thermodynamic (base-stacking calculated) T_m (melting temperature)
// Input: DnaConc is the primer concentration, nM
// SaltConc is monovalent cation (K+ and Na+) concentration, mM
// MgConc, mM
// Return: The melting temperature, in C^0
// Requires: strlen (seq) is between 7 and 35
// From: http://www-genome.wi.mit.edu/ftp/distribution/software/primer.0.5/primer.c,
// now Primer3 (http://frodo.wi.mit.edu/primer3/primer3_code.html)
// VectorNTI makes the same results
PRIMER* MakePrimer (size_t PrimerLen,
size_t SearchStart,
size_t SearchEnd,
PHRED_SCORE MinQuality,
uint MaxMaxRepeat,
PROBABILITY MaxGCShare,
double DnaConcentration,
double SaltConcentration,
double MgConcentration,
double MinMeltTemp,
double MaxMeltTemp,
double TargetMeltTemp) const;
// From 5' to 3'
// Return: Best primer, May be nullptr
// Primer inside the segment [SearchStart, SearchEnd]
// Requires: TargetMeltTemp between MinMeltTemp and MaxMeltTemp
// Invokes: GetMeltTemp ()
PROBABILITY NucleotideFreqFrame (size_t Start,
Frame frame,
size_t Count,
const char* Alphabet) const;
void GetOpenFrameProb (size_t Start,
size_t Count,
PROBABILITY FrameProb [3]) const;
// Output: FrameProb []
// Author: Max Troukhan
bool GetOrf (int &CDS_Start,
bool &FL5,
int &CDS_End,
bool &FL3,
const CodStatistics* StatTable,
double Stress) const;
// Output: CDS_Start|End - may be outside seq
// CDS_End - next position after the last known codon of the CDS
// FL5|3
// Valid if result is true
// CDS_Start < CDS_End
// Return: true if Orf is found
double CompareOrfs (const CodStatistics* StatTable1,
const CodStatistics* StatTable2) const;
// Return: Positive iff seq is more probable to be of organism of StatTable1
// CompareOrfs (a,b) = - CompareOrfs (b,a)
double Orf2Strand (const CodStatistics* StatTable) const;
// Return: Positive iff the positive strand of seq is more probable than the negative strand
// Orf2Strand (a) = - Orf2Strand (Reverse(a))
// Input: Neightborhood: to search start/stop codon, in nts
// Output: if true then CDS_Start < CDS_End and (CDS_End - CDS_Start) % 3 = 0
// Return: true iff FL
bool CDS_Start_nr2Orf (int CDS_Start_nr,
int Neighborhood,
int &CDS_Start,
int &CDS_End) const;
bool CDS_End_nr2Orf (int CDS_End_nr,
int Neighborhood,
int &CDS_Start,
int &CDS_End) const;
// Output: CDS_Start: minimum possible
#endif
};
struct FastaDna final : Dna
{
FastaDna (const string &fName,
size_t reserveLen,
bool sparse_arg)
: Dna (* unique_ptr<LineInput> (getLineInput (fName)), reserveLen, sparse_arg)
{}
};
#if 0
class DNA_COLLECTION: public _SEQ_COLLECTION
// of Dna*
{
typedef _SEQ_COLLECTION inherited;
public:
DNA_COLLECTION (): inherited () {}
DNA_COLLECTION (const char* FName,
bool GapCoded);
Dna* GetDna (size_t i) const
{ return (Dna*) GetSeq (i); }
void SaveQual (const char* FName,
uint DefaultQualScore) const;
};
#endif
/////////////////////////// Peptide ///////////////////////////////
size_t aa2num (char wildAminoacid);
// Return: if wildAminoacid is in peptideAlphabet then position in peptideAlphabet
// else if wildAminoacid is terminator then 20
// else if wildAminoacid is in peptideWildcards then 21
// else error
// Case-insensitive
bool moreGeneralAminoacid (char wildAminoacid1,
char wildAminoacid2);
// Return: true if the aminoacids of wildAminoacid1 is a superset of those of wildAminoacid2
// (i.e., wildAminoacid1 is more general than or equal to wildAminoacid2)
// Requires: wildAminoacid1|2 in extTermPeptideAlphabet
inline bool aaMatch (char aa1,
char aa2)
{ return moreGeneralAminoacid (aa1, aa2)
|| moreGeneralAminoacid (aa2, aa1);
}
typedef double AlignScore;
constexpr AlignScore score_inf = numeric_limits<AlignScore>::max ();
struct SubstMat final : Root
// Substitution matrix for protein alignment
// NCBI: e.g., /am/ftp-blast/matrices/BLOSUM62
/* ------ default -----
matrix gap_open gap_extent
-------- -------- ----------
BLOSUM90 10 1
BLOSUM80 10 1
BLOSUM62 11 1
BLOSUM50 13 2
BLOSUM45 14 2
PAM250 14 2
PAM70 10 1
PAM30 9 1
IDENTITY 15 2
*/
{
static constexpr const char* chars {"ARNDCQEGHILKMFPSTWYVBZX*"};
static constexpr size_t sim_size = 128;
AlignScore sim [sim_size] [sim_size];
SubstMat () = default;
explicit SubstMat (const string &fName);
void qc () const override;
void saveText (ostream& os) const override;
bool goodIndex (size_t i) const
{ return sim [i] [i] == sim [i] [i]; } // Not a NaN
void printAnomalies () const;
AlignScore getSubstitutionDist (size_t row,
size_t col) const
{ return sim [row] [row] + sim [col] [col] - 2 * sim [row] [col]; }
AlignScore getDeletionDist (size_t row,
AlignScore gap_sim) const
{ return sim [row] [row] - 2 * gap_sim; }
AlignScore char2score (char c1,
char c2) const;
};
struct PeptideOrf final : Root
// DNA -> translation of a segment -> ORF
{
size_t translationStart {no_index};
// Start of the peptide translation
// !strand => !translationStart
Strand strand {0};
// In the translation which starts from translationStart
size_t start {no_index};
// May be: no_index
bool startM {false};
// Peptide::isStartAa(peptide->seq[start])
size_t stop {no_index};
// >= start
bool stopTerminator {false};
// peptide->seq[stop] == *terminator
PeptideOrf (size_t translationStart_arg,
Strand strand_arg,
const Peptide* peptide,
size_t start_arg);
// Input: peptide: DNA segment translation
PeptideOrf (size_t translationStart_arg,
Strand strand_arg,
size_t start_arg,
bool startM_arg,
size_t stop_arg,
bool stopTerminator_arg)
: translationStart (translationStart_arg)
, strand (strand_arg)
, start (start_arg)
, startM (startM_arg)
, stop (stop_arg)
, stopTerminator (stopTerminator_arg)
{}
// In peptide translated from the DNA
explicit PeptideOrf (istream &is)
{ int iStrand;
is >> translationStart >> iStrand >> start >> stop >> startM >> stopTerminator;
strand = (char) iStrand;
}
PeptideOrf () = default;
void qc () const override;
void saveText (ostream &os) const override
{ os << translationStart
<< '\t' << (int) strand
<< '\t' << start
<< '\t' << stop
<< '\t' << startM
<< '\t' << stopTerminator;
}
// Requires: !empty()
bool empty () const override
{ return start == no_index; }
bool good (size_t size_min) const
{ return ! empty ()
&& startM
&& stopTerminator
&& size () >= size_min;
}
// Requires; !empty()
size_t size () const
{ return stop - start; }
// Without the terminator
size_t dnaPos (size_t pos) const
{ const size_t dnaLen = 3 * pos;
return strand == 1 ? (translationStart + dnaLen) : (translationStart - dnaLen);
}
// Requires: (bool)frame
size_t cdsStart () const
{ return dnaPos (start); }
size_t cdsStop () const
{ return dnaPos (stop + stopTerminator); }
Peptide* toPeptide (const Peptide* peptide) const;
// Input: peptide: used in Peptide::getOrfs()
};
struct Peptide : Seq
{
static constexpr const size_t stdAveLen {400}; // PAR
static constexpr double stdMinComplexity {2.5}; // PAR
bool pseudo {false};
Peptide () = default;
Peptide (const string &name_arg,
size_t seqLen,
bool sparse_arg)
: Seq (name_arg, seqLen, sparse_arg)
{}
Peptide (const string &name_arg,
const string &seq_arg,
bool sparse_arg)
: Seq (name_arg, seq_arg, sparse_arg)
{}
Peptide (LineInput &fasta,
size_t reserveLen,
bool sparse_arg)
: Seq (fasta, reserveLen, sparse_arg, true)
{}
Peptide (Multifasta &fasta,
size_t reserveLen,
bool sparse_arg);
Peptide* copy () const final
{ return new Peptide (*this); }
void qc () const override;
void saveText (ostream& os) const override
{ printCase (os, true); }
const Peptide* asPeptide () const final
{ return this; }
const char* getSeqAlphabet () const final
{ return sparse ? extSparseTermPeptideAlphabet : extTermPeptideAlphabet; }
bool isAmbiguous (char c) const final
{ return c == 'X'; }
bool hasInsideStop () const
{ const size_t pos = seq. find ('*');
return pos != string::npos && pos != seq. size () - 1;
}
bool trimStop ()
{ return trimSuffix (seq, "*"); }
bool isDescriptionPartial () const;
static bool isStartAa (char aa)
{ return aa != '*' && isLower (aa); }
// Requires: after codon2aa(,,true)
Vector<PeptideOrf> getPeptideOrfs (size_t translationStart,
Strand strand,
bool includeInitial,
bool longestOnly,
size_t len_min) const;
double getComplexityInt (size_t start,
size_t end) const final;
// Return: >= 0; -1 <=> seq has an amino acid not in *peptideAlphabet
double getSelfSimilarity (const SubstMat &mat,
size_t start = 0,
size_t stop = 0) const;
// Input: start, stop = 0 => whole sequence
double getSimilarity (const Peptide &other,