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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/aln__scanner__sequin_8cpp_source.html below:

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

64  bool

processingData =

true

;

65  bool

inFirstBlock =

false

;

69  while

(iStr.

ReadLine

(line, lineCount)) {

75  if

(lineInBlock !=

mSeqIds

.size()) {

77  "Missing data line. Expected sequence data for seqID \"%s\""

,

78  mSeqIds

[lineInBlock].mData.c_str());

84

processingData =

false

;

86

inFirstBlock =

false

;

97  "Missing data line. Expected sequence data, not sequence offsets"

);

103  if

(processingData) {

107  "Missing data line. Expected sequence data, not termination line"

);

113  if

(!processingData) {

114

processingData =

true

;

118

inFirstBlock =

true

;

121  string

seqId, seqData;

126  "Malformatted data line"

);

139  "Duplicate sequence ID \"%s\", first seen on line %d"

,

140

seqId.c_str(), existingInfo.

mNumLine

);

144  "Conflicting IDs: \"%s\" differs only in case from \"%s\" on line %d."

,

145

seqId.c_str(), existingInfo.

mData

.c_str(), existingInfo.

mNumLine

);

152  mSeqIds

.push_back({seqId, lineCount});

156  if

(lineInBlock >=

mSeqIds

.size()) {

160  "Extraneous data line in interleaved data block"

);

164  "Unexpected sequence ID \"%s\""

, seqId.c_str());

173  if

(refSeqData.empty()) {

174

refSeqData = seqData;

177  if

(seqData.size() != refSeqData.size()) {

179  "Unexpected number of sequence symbols (expected %d but found %d)"

,

180

refSeqData.size(), seqData.size());

186  for

(

auto i

= 0;

i

< seqData.size(); ++

i

) {

187  if

(seqData[

i

] ==

'.'

) {

188

seqData[

i

] = refSeqData[

i

];

193  mSequences

[lineInBlock].push_back({seqData, lineCount});

215

vector<string> tokens;

217  if

(tokens.size() > 5) {

220  for

(

auto

token: tokens) {

234  return

(line ==

"//"

);

245

vector<string> tokens;

247  if

(tokens.size() < 2) {

254  if

(tokens[1] ==

">"

) {

255  if

(tokens.size() < 5) {

259  for

(

auto

curBlock = 3; curBlock < tokens.size() - 1; ++curBlock) {

260

seqData += tokens[curBlock];

264  for

(

auto

curBlock = 1; curBlock < tokens.size(); ++curBlock) {

265

seqData += tokens[curBlock];

END_ENUM_INFO string ErrorPrintf(const char *format,...)

void xImportAlignmentData(CSequenceInfo &, CLineInput &) override

static bool xExtractSequinSequenceData(const string &line, string &seqId, string &seqData)

static bool xIsSequinOffsetsLine(const string &line)

static bool xIsSequinTerminationLine(const string &line)

void xAdjustSequenceInfo(CSequenceInfo &) override

bool xSeqIdIsEqualToInfoAt(const string &seqId, int index)

vector< TLineInfo > mSeqIds

vector< vector< TLineInfo > > mSequences

ESeqIdComparison xGetExistingSeqIdInfo(const string &seqId, TLineInfo &existingInfo)

virtual bool ReadLine(string &line, int &lineNum)=0

CSequenceInfo & SetBeginningGap(const string &c)

CSequenceInfo & SetEndGap(const string &c)

CSequenceInfo & SetMiddleGap(const string &c)

CSequenceInfo & SetMatch(const string &c)

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 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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

Truncate whitespace in a string (in-place)

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eAlnSubcode_IllegalDataLine

@ eAlnSubcode_BadDataCount

@ eAlnSubcode_MissingDataLine

@ eAlnSubcode_UnexpectedSeqId


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