RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/aln__util_8cpp_source.html below:

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

48 const

vector<SLineInfo>& orderedIds,

56 if

((orderedIds.size() > idCount) &&

57

seqId == orderedIds[idCount].mData) {

62 string

seqIdLower(seqId);

65 auto

it = orderedIds.begin();

66 bool

exactCopy =

false

;

67 while

(it != orderedIds.end()) {

68 if

(it->mData == seqId) {

72 auto

orderedIdLower(it->mData);

74 if

(orderedIdLower == seqIdLower) {

82 if

(it != orderedIds.end()) {

85 "Duplicate ID: \"%s\" has already appeared in this block, on line %d."

, seqId.c_str(), it->mNumLine);

89 "Conflicting IDs: \"%s\" differs only in case from \"%s\", which has already appeared in this block, on line %d."

, seqId.c_str(), it->mData.c_str(), it->mNumLine);

100 if

(it == orderedIds.end()) {

102 "Inconsistent sequence_IDs in the data blocks. Each data block must contain the same set of sequence_IDs."

);

110 auto

idPos = distance(orderedIds.begin(), it);

111 if

(idPos < idCount) {

114 "Duplicate ID: \"%s \" has already appeared in this block, on line %d."

115

seqId.c_str(), it->mNumLine);

119 "Conflicting IDs: \"%s\" differs only in case from \"%s\", which has already appeared in this block, on line %d."

, seqId.c_str(), it->mData.c_str(), it->mNumLine);

123 if

(idPos == idCount) {

125 "Inconsistent ID case: \"%s\" differs in case from \"%s\" used to identify this sequence in the first block."

126

seqId.c_str(), it->mData.c_str());

130

description =

"Sequence_IDs are in different orders in the data blocks in your file. The sequences and sequence_IDs are expected to be in the same order in each block."

;

144 string

& defLineInfo)

151 "Deflines were detected in your file, however some lines are missing the \'>\' character at the beginning of the line. Each defline must begin with \'>\'."

);

153 auto

dataStart = line.find_first_not_of(

" \t"

, 1);

154 if

(dataStart == string::npos) {

158 "Bad defline line: Should not be empty"

);

160 string

defLine = line.substr(dataStart);

163

defLineInfo = defLine;

174 const string

& dataLine,

182 if

(tokens.size() < 2) {

186 "Bad data line: Expected \"<seqId> <data> <offset>\""

);

188

seqId = tokens.front();

190 if

(tokens.back().find_first_not_of(

"0123456789"

) == string::npos) {

204 const string

& dataLine,

211 if

(tokens.size() < 2) {

215 "Bad data line: Expected \"<seqId> <data> <offset>\""

);

217

seqId = tokens.front();

230

vector<string> splits;

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

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 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 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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case â string& version.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

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

void CheckId(const string &seqId, const vector< SLineInfo > &orderedIds, int idCount, int lineNum, bool firstBlock)

void ProcessDefline(const string &defLine, string &seqId, string &defLineInfo)

void ProcessDataLine(const string &dataLine, string &seqId, string &seqData, int &offset)

@ eAlnSubcode_BadSequenceCount

@ eAlnSubcode_IllegalDataLine

@ eAlnSubcode_UnexpectedSeqId

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4