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NCBI C++ ToolKit: include/algo/gnomon/pcsf.hpp Source File

43 typedef

pair<TSignedSeqPos, TPhyloCSFScore>

TElement

;

45

m_scores.resize(

len

);

46 if

(!from.read(

reinterpret_cast<char

>

(m_scores.data()),

len

sizeof

(

TElement

))) {

47

cerr <<

"Error in PhyloCSF compact read\n"

;

52 if

out

.write(

reinterpret_cast<const char

>

(m_scores.data()), Size()*

sizeof

(

TElement

))) {

53

cerr <<

"Error in PhyloCSF compact write\n"

;

58 auto

rslt = lower_bound(m_scores.begin(), m_scores.end(), p, [](

const TElement

& e,

TSignedSeqPos i

) { return e.first < i; });

59 if

(rslt == m_scores.end() || rslt->first != p)

66 size_t Size

()

const

{

return

m_scores.size(); }

73 if

(

m_map

nullptr

) {

82 if

(

m_map

nullptr

) {

84 if

(edited_range.

Empty

())

88 if

(orig_range.

Empty

())

90 size_t

left = (*m_scoresp)[s].LowerBound(orig_range.

GetFrom

()+

m_shift

);

94 size_t

right = (*m_scoresp)[s].UpperBound(orig_range.

GetTo

()+

m_shift

)-1;

112 if

(!from.read(

reinterpret_cast<char

>

(&data_length),

sizeof

data_length)) {

113

cerr <<

"Error in PhyloCSF read\n"

;

117

from.seekg(data_length, ios_base::cur);

119 while

(from.read(

reinterpret_cast<char

>

(&slen),

sizeof

slen)) {

120

vector<char>

buf

(slen);

121

from.read(

buf

.data(), slen);

122 string

contig_acc(

buf

.begin(),

buf

.end());

124

from.read(

reinterpret_cast<char

>

(&shift),

sizeof

(

size_t

));

126

from.read(

reinterpret_cast<char

>

(&plus_len),

sizeof

(

TSignedSeqPos

));

128

from.read(

reinterpret_cast<char

>

(&minus_len),

sizeof

(

TSignedSeqPos

));

130

cerr <<

"Error in PhyloCSF index read\n"

;

133

index[contig_acc] = make_tuple(shift, plus_len, minus_len);

138 for

(

auto

& ind : index) {

139 auto

& contig_acc = ind.first;

140 auto

shift = get<0>(ind.second);

141 auto

plus_len = get<1>(ind.second);

142 auto

minus_len = get<2>(ind.second);

143

from.seekg(shift,ios_base::beg);

149 size_t

data_length = 0;

151

data_length += (scr.second[0].Size()+scr.second[1].Size());

154 out

.write(

reinterpret_cast<const char

>

(&data_length),

sizeof

data_length);

157 for

(

int

strand = 0; strand < 2; ++strand)

158

scr.second[strand].Write(

out

);

161 size_t

shift =

sizeof

data_length;

163 auto

& contig_acc = scr.first;

165 int

slen = (

int

)contig_acc.size();

166 out

.write(

reinterpret_cast<const char

>

(&slen),

sizeof

slen);

167 out

.write(contig_acc.c_str(), slen);

169 out

.write(

reinterpret_cast<const char

>

(&shift),

sizeof

shift);

170 for

(

int

strand = 0; strand < 2; ++strand) {

172 out

.write(

reinterpret_cast<const char

>

len

sizeof len

);

177

cerr <<

"Error in PhyloCSF write\n"

;

192 for

(

auto

& cs : scores) {

193 auto

& contig_acc = cs.first;

194 for

(

int

strand = 0; strand < 2; ++strand) {

196 auto

scr = cs.second[strand][

];

TSignedSeqRange ShrinkToRealPointsOnEdited(TSignedSeqRange edited_range) const

TSignedSeqRange MapRangeEditedToOrig(TSignedSeqRange edited_range, bool withextras=true) const

TSignedSeqPos MapEditedToOrig(TSignedSeqPos edited_pos) const

void CompactFullScores(const map< string, array< TFVec, 2 >> &scores)

void Read(CNcbiIstream &from)

SPhyloCSFSlice * CreateSliceForContig(const string &contig_acc) const

map< string, array< SPhyloCSFCompactScore, 2 > > m_contig_scores

void Write(CNcbiOstream &out) const

const_iterator end() const

const_iterator find(const key_type &key) const

std::ofstream out("events_result.xml")

main entry point for tests

int TSignedSeqPos

Type for signed sequence position.

static TThisType GetEmpty(void)

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

vector< TPhyloCSFScore > TFVec

size_t UpperBound(TSignedSeqPos p) const

void Write(CNcbiOstream &out) const

void Read(CNcbiIstream &from, size_t len)

pair< TSignedSeqPos, TPhyloCSFScore > TElement

size_t LowerBound(TSignedSeqPos p) const

TPhyloCSFScore Score(TSignedSeqPos p) const

vector< TElement > m_scores

TSignedSeqRange CompactRange(int s, TSignedSeqRange edited_range) const

TPhyloCSFScore Score(int s, TSignedSeqPos codon_left) const

const array< SPhyloCSFCompactScore, 2 > * m_scoresp

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