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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnvecprint_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/alnvecprint.cpp Source File

101

vector<string>

buffer

(nrows);

108  int

seg, pos, left_seg = -1, right_seg = -1;

113  for

(seg = nsegs - 1, pos = seg * nrows +

row

;

114

seg >= 0; --seg, pos -= nrows) {

115  if

(starts[pos] >= 0) {

121  for

(seg = 0, pos =

row

; seg < nsegs; ++seg, pos += nrows) {

123  if

((start = starts[pos]) >= 0) {

134  char

* ch_buff =

new char

[

len

+1];

136  if

(left_seg < 0 || seg > right_seg && right_seg > 0) {

141

memset(ch_buff, fill_ch,

len

);

163  if

(pos + scrn_width > aln_len) {

164

scrn_width = aln_len - pos;

166

}

while

(pos < aln_len);

176

rng.

Set

(aln_pos, aln_pos + scrn_width - 1);

179

aln_seq_str.reserve(scrn_width + 1);

193

aln_pos += scrn_width;

201

vector<string>

buffer

(nrows);

202

vector<CAlnMap::TSeqPosList> insert_aln_starts(nrows);

203

vector<CAlnMap::TSeqPosList> insert_starts(nrows);

204

vector<CAlnMap::TSeqPosList> insert_lens(nrows);

205

vector<CAlnMap::TSeqPosList> scrn_lefts(nrows);

206

vector<CAlnMap::TSeqPosList> scrn_rights(nrows);

213

&insert_aln_starts[

row

],

214

&insert_starts[

row

],

218

&scrn_rights[

row

]);

230

<< scrn_rights[

row

].front()

232

scrn_lefts[

row

].pop_front();

233

scrn_rights[

row

].pop_front();

237  if

(pos + scrn_width > aln_len) {

238

scrn_width = aln_len - pos;

240

}

while

(pos < aln_len);

254

*

m_Out

<<

"CLUSTAL W (1.83) multiple sequence alignment"

<< endl << endl;

272  int

seg, pos, left_seg = -1, right_seg = -1;

279  if

(starts[pos] >= 0) {

285  for

(seg = 0, pos =

row

; seg < nsegs; ++seg, pos +=

m_NumRows

) {

287  if

((start = starts[pos]) >= 0) {

298  char

* ch_buff =

new char

[

len

+1];

300  if

(left_seg < 0 || seg > right_seg && right_seg > 0) {

305

memset(ch_buff, fill_ch,

len

);

314  for

(

TSeqPos

pos = 0; pos < aln_len; pos++) {

315  bool

identity =

true

;

316  char

residue =

buffer

[0][pos];

339

aln_pos += scrn_width;

340  if

(aln_pos + scrn_width > aln_len) {

341

scrn_width = aln_len - aln_pos;

343

}

while

(aln_pos < aln_len);

352  string

identities_str;

353

identities_str.reserve(scrn_width + 1);

357

rng.

Set

(aln_pos,

min

(aln_pos + scrn_width - 1, aln_stop));

360

aln_seq_str.reserve(scrn_width + 1);

369

identities_str = aln_seq_str;

371  for

(

size_t i

= 0;

i

< aln_seq_str.length();

i

++) {

372  if

(aln_seq_str[

i

] != identities_str[

i

]) {

373

identities_str[

i

] =

' '

;

378  for

(

size_t i

= 0;

i

< identities_str.length();

i

++) {

379  if

(identities_str[

i

] !=

' '

) {

380

identities_str[

i

] =

'*'

;

385

*

m_Out

<< identities_str

387

aln_pos += scrn_width;

407  for

(pos = 0; pos < aln_len; pos++) {

408  bool

identity =

true

;

409  char

residue =

buffer

[0][pos];

434  if

(pos + scrn_width > aln_len) {

435

scrn_width = aln_len - pos;

437

}

while

(pos < aln_len);

void PrintId(CAlnMap::TNumrow row) const

Field printers.

const CAlnMap::TNumrow m_NumRows

void PrintNumRow(CAlnMap::TNumrow row) const

void PrintSeqPos(TSeqPos pos) const

int GetWidth(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TSeqPos GetAlnStop(TNumseg seg) const

CDense_seg::TNumseg TNumseg

const CDense_seg & GetDenseg(void) const

TNumseg GetNumSegs(void) const

void PopsetStyle(int scrn_width=70, EAlgorithm algorithm=eUseAlnSeqString)

Printing methods.

EAlgorithm

which algorithm to choose

@ eUseWholeAlnSeqString

memory efficient, recommended for large alns

@ eUseAlnSeqString

memory ineficient

CAlnVecPrinter(const CAlnVec &aln_vec, CNcbiOstream &out)

Constructor.

void ClustalStyle(int scrn_width=50, EAlgorithm algorithm=eUseAlnSeqString)

bool IsSetEndChar() const

TResidue GetGapChar(TNumrow row) const

string & GetSeqString(string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const

void SetEndChar(TResidue gap_char)

TResidue GetEndChar() const

void SetGapChar(TResidue gap_char)

bool IsSetGapChar() const

string & GetWholeAlnSeqString(TNumrow row, string &buffer, TSeqPosList *insert_aln_starts=0, TSeqPosList *insert_starts=0, TSeqPosList *insert_lens=0, unsigned int scrn_width=0, TSeqPosList *scrn_lefts=0, TSeqPosList *scrn_rights=0) const

string & GetAlnSeqString(string &buffer, TNumrow row, const CAlnMap::TSignedRange &aln_rng) const

@ eLeft

Towards lower aln coord (always to the left)

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

TThisType & Set(position_type from, position_type to)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

Magic spell ;-) needed for some weird compilers... very empiric.

#define row(bind, expected)

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