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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/aln__formatguess_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/aln_formatguess.cpp Source File

50

vector<string> testSample;

53 if

(testSample.empty()) {

82

vector<string>& testSample)

91

testSample.push_back(testLine);

106 string

testLine = sample[0];

123 const string

CONSENSUS_CHARS =

" .:*"

;

125 string

testLine = sample[0];

133 size_t

lineCount = 0;

134 size_t

blockCount = 0;

135 while

(blockCount < 3) {

137 if

(lineCount < sample.size()) {

138

line = sample[lineCount];

142

sample.push_back(line);

144 if

(lineCount > 0 && line.empty()) {

145 auto

maybeConsensus = sample[lineCount-1];

147 auto

firstConsensusChar = maybeConsensus.find_first_of(

148

CONSENSUS_CHARS.substr(1));

149 if

(firstConsensusChar == string::npos) {

152 auto

firstNonConsensusChar = maybeConsensus.find_first_not_of(

154 if

(firstNonConsensusChar != string::npos) {

176 for

( ;

< sample.size(); ++

) {

181 if

(

< sample.size()) {

199 string

testLine = sample[0];

200

vector<string> tokens;

202 if

(tokens.size() != 2) {

205 if

(tokens.front().find_first_not_of(

"0123456789"

) != string::npos) {

208 if

(tokens.back().find_first_not_of(

"0123456789"

) != string::npos) {

225 if

(!sample[0].

empty

()) {

229

vector<string> tokens;

231 if

(tokens.empty()) {

234 for

(

size_t

index = 0; index < tokens.size(); ++index) {

236 if

(

offset

!= 10 + 10*index) {

254 size_t

lineIndex = 0;

258 if

(sample.size() < lineIndex + 4) {

261 if

(!sample[lineIndex].

empty

()) {

266

vector<string> tokens;

268 if

(tokens.size() != 2) {

271 int

startOffset(0), endOffset(0);

276 catch

(std::exception&) {

279 if

(startOffset != 1) {

282 if

(endOffset > 50) {

287

list<string> dataColumns;

289 if

(dataColumns.size() < 2) {

292

dataColumns.pop_front();

293 string

seqData =

NStr::Join

(dataColumns.begin(), dataColumns.end(),

""

);

294 int

dataSize = seqData.size();

295 return

(dataSize == (endOffset - startOffset + 1));

bool xSampleIsSequin(const TSample &)

bool xSampleIsFastaGap(const TSample &)

EAlignFormat GetFormat(CPeekAheadStream &iStr)

bool xSampleIsPhylip(const TSample &)

bool xSampleIsNexus(const TSample &)

void xInitSample(CPeekAheadStream &iStr, TSample &sample)

static const int SAMPLE_SIZE

bool xSampleIsMultAlign(const TSample &)

bool xSampleIsClustal(TSample &, CPeekAheadStream &iStr)

bool PeekLine(string &str)

The NCBI C++ standard methods for dealing with std::string.

#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.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static string & ToLower(string &str)

Convert string to lower case â string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

constexpr bool empty(list< Ts... >) noexcept

static PCRE2_SIZE * offsets

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