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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/aln__printer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/align_format/aln_printer.cpp Source File

49 for

(

size_t i

=0;

str

.length();

++) {

61 if

((*it)->IsTitle()) {

62 if

(!retval.empty()) {

65

retval += (*it)->GetTitle();

87

retval =

id

->AsFastaString();

98

: m_AlnVec(new

CAlnVec

(seqalign.GetSegs().GetDenseg(), scope)),

139 for

(

int i

=0;

< num_seqs;

++) {

161 const

vector<CSeq_id_Handle>& ids = bhandle.

GetId

();

162 ITERATE

(vector<CSeq_id_Handle>, it, ids) {

163

ostr << it->GetSeqId()->AsFastaString();

164 if

(it + 1 != ids.end()) {

170 if

(!title.empty()) {

171

ostr <<

" "

<< title;

177 for

(

int

j=0;j < (

int

)seq.length();j++) {

178 if

(j %

m_Width

== 0 && j != 0) {

199 const unsigned int

kSeqTitleWidth = 10;

204

ostr <<

" "

<< num_sequences <<

" "

<< sequence.length() <<

NcbiEndl

;

207 for

(

int i

=0;

< num_sequences;

++) {

215 if

(seq_title.length() > kSeqTitleWidth) {

216

seq_title.erase(kSeqTitleWidth - 1, seq_title.size() - 1);

219 while

(seq_title.length() < kSeqTitleWidth) {

230 for

(j=0;j < sequence.length() && j <

m_Width

- kSeqTitleWidth;j++) {

233 for

(;j < sequence.length();j++) {

234 if

((j + kSeqTitleWidth) %

m_Width

== 0 && j != 0) {

248 const unsigned int

kSeqTitleWidth = 10;

252

ostr <<

" "

<< num_sequences <<

" "

<< aln_width <<

NcbiEndl

;

255 for

(

int i

=0;

< num_sequences;

++) {

263 if

(seq_title.length() > kSeqTitleWidth) {

264

seq_title.erase(kSeqTitleWidth - 1, seq_title.size() - 1);

267 while

(seq_title.length() < kSeqTitleWidth) {

274 min

(

m_Width

- (

int

)kSeqTitleWidth, aln_width)));

280 int

from =

m_Width

- kSeqTitleWidth;

281 while

(from < (

int

)aln_width) {

283 for

(

int i

=0;

< num_sequences;

++) {

302

vector<string> seqids(num_sequences);

303 int

max_id_length = 0;

304 for

(

int i

=0;

< num_sequences;

++) {

307 if

((

int

)seqids[

].length() > max_id_length) {

308

max_id_length = seqids[

].length();

314

"DIMENSIONS ntax="

<< num_sequences <<

" nchar=" 315

<< last_pos + 1 <<

";" 317

"FORMAT datatype=" 326 int

seqid_width = max_id_length + 2;

327 while

(from < last_pos) {

329 for

(

int i

=0;

< num_sequences;

++) {

332 int

margin = seqid_width - seqids[

].length();

static void s_ReplaceNonAlphaNum(string &str)

static string s_GetLabel(const CBioseq_Handle &bhandle)

static string s_GetTitle(const CBioseq_Handle &bhandle)

USING_SCOPE(align_format)

const CSeq_id & GetSeqId(TNumrow row) const

TDim GetNumRows(void) const

TSeqPos GetAlnStop(TNumseg seg) const

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

TResidue GetGapChar(TNumrow row) const

void SetEndChar(TResidue gap_char)

void SetGapChar(TResidue gap_char)

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

CScope & GetScope(void) const

void SetAaCoding(TCoding coding)

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

Printer for popular multiple alignmnet formats.

CMultiAlnPrinter(const CSeq_align &seqalign, CScope &scope, EAlignType type=eNotSet)

Constructor.

void x_PrintPhylipSequential(CNcbiOstream &ostr)

Print alignment in Phylip format with sequetial sequences.

void x_PrintNexus(CNcbiOstream &ostr)

Print alignment in Nexus format.

EAlignType

Alignment display type for showing nucleotice or protein-related information.

int m_Width

Selected width of the text field.

void Print(CNcbiOstream &ostr)

Print alignment.

CRef< CAlnVec > m_AlnVec

Alignment manager.

EFormat m_Format

Selected alignment format.

void x_PrintClustal(CNcbiOstream &ostr)

Print alignment in ClustalW format.

void x_PrintPhylipInterleaved(CNcbiOstream &ostr)

Print alignment in Phylip format with interleaved sequences.

EAlignType m_AlignType

Alignment type.

void x_PrintFastaPlusGaps(CNcbiOstream &ostr)

Print alignment in fasta + gaps format.

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ eContent

Untagged human-readable accession or the like.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

const TDescr & GetDescr(void) const

const TId & GetId(void) const

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static const char label[]

bool IsStr(void) const

Check if variant Str is selected.

bool IsId(void) const

Check if variant Id is selected.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

list< CRef< CSeqdesc > > Tdata

const Tdata & Get(void) const

Get the member data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

unsigned int

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

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