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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/aln__scanner__fastagap_8cpp_source.html below:

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

69  const string

& rawDefStr,

74  string

defStr = rawDefStr.substr(1);

86  bool

waitingForSeqData =

false

;

87

vector<unsigned> expectedDataSizes;

88  unsigned

currentDataLineIndex = 0;

89  bool

processingFirstSequence =

true

;

90  unsigned

expectedNumLines = 0;

94  while

(iStr.

ReadLine

(line, lineNumber)) {

100  if

(waitingForSeqData) {

102

waitingForSeqData =

false

;

103

processingFirstSequence =

false

;

108  if

(processingFirstSequence) {

109

expectedDataSizes.push_back(seqData.size());

113  if

(!expectedNumLines) {

114

expectedNumLines =

static_cast<unsigned>

(expectedDataSizes.size());

116  auto

currentDataSize = seqData.size();

117  auto

expectedDataSize = (currentDataLineIndex < expectedNumLines) ?

118

expectedDataSizes[currentDataLineIndex] :

120  if

(currentDataSize != expectedDataSize) {

130  mSequences

.back().push_back({seqData, lineNumber});

131

currentDataLineIndex++;

145  "Invalid Fasta definition line. \">\" must be followed by a sequence_ID."

);

155  "Duplicate ID: \"%s\" has already appeared at line %d."

,

156

seqId.c_str(), existingInfo.

mNumLine

);

160  "Conflicting IDs: \"%s\" differs only in case from \"%s\" at line %d."

,

161

seqId.c_str(), existingInfo.

mData

.c_str(), existingInfo.

mNumLine

);

169  mSeqIds

.push_back({seqId, lineNumber});

170  mDeflines

.push_back({defLine, lineNumber});

172

waitingForSeqData =

true

;

173

currentDataLineIndex = 0;

string BadCharCountPrintf(int expectedCount, int actualCount)

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

static void sSplitFastaDef(const string &rawDefStr, string &seqId, string &defLine)

void xImportAlignmentData(CSequenceInfo &, CLineInput &) override

vector< TLineInfo > mSeqIds

vector< vector< TLineInfo > > mSequences

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

vector< TLineInfo > mDeflines

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

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

Truncate whitespace in a string (in-place)

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

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

void StripBlanks(const string &line, string &stipped)

@ eAlnSubcode_BadDataCount

@ eAlnSubcode_UnexpectedSeqId

@ eAlnSubcode_IllegalDefinitionLine

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