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

71 string

lastLine = args.back().mData;

72 auto

lastWhiteSpacePos = lastLine.find_last_of(

" \t"

);

73 string

lastToken = (lastWhiteSpacePos ==

NPOS

) ?

75

lastLine.substr(lastWhiteSpacePos);

77 string

lastTokenLower(lastToken);

80 if

(lastTokenLower ==

"end"

) {

81 const bool

onlyArg = (args.size() == 1 &&

82

lastWhiteSpacePos ==

NPOS

);

87 "\""

+ lastToken +

"\" is not a valid argument for the \""

88 command

.name +

"\" command."

);

95 "File format autocorrected to comply with Nexus rules. Unexpected \"end;\". Appending \';\' to prior command. No action required."

);

97 if

(lastWhiteSpacePos ==

NPOS

) {

102

args.back().mData.substr(0, lastWhiteSpacePos));

121

commandTokens.front().mData.find_first_of(

" \t["

);

122 if

(nameEnd ==

NPOS

) {

131 command

.startLineNum = commandTokens.front().mNumLine;

133 string

nameLower =

command

.name;

137 if

(nameLower ==

"begin"

) {

152 "\""

command

.name +

"\" command appears outside of block."

);

157 if

(block ==

"ncbi"

) {

162 if

(nameLower ==

"end"

) {

168 "\" command terminates a block and does not take any arguments."

);

174 if

(block ==

"data"

175

block ==

"characters"

) {

180 if

(block ==

"taxa"

) {

194 auto

nameLower =

command

.name;

200 if

(nameLower ==

"dimensions"

) {

204 if

(nameLower ==

"format"

) {

208 if

(nameLower ==

"matrix"

) {

227 auto

nameLower =

command

.name;

233 if

(nameLower ==

"dimensions"

) {

253 static string

previousCommand;

255 auto

nameLower =

command

.name;

257 if

(nameLower ==

"end"

) {

258 if

(previousCommand !=

"sequin"

) {

260 "Exiting empty \"NCBI\" block. Expected a \"sequin\" command."

;

266

previousCommand.clear();

273 if

(nameLower ==

"sequin"

) {

275

previousCommand =

"sequin"

;

281 "Unexpected \""

command

.name +

"\" command inside \"NCBI\" block. The \"NCBI\" block must contain a \"sequin\" command and no other commands."

);

285

previousCommand.clear();

298 for

(

auto

lineInfo : args) {

299 auto

line = lineInfo.mData;

300 auto

lineNum = lineInfo.mNumLine;

301 string dummy

, defLine;

310 if

dummy

.empty()) {

312 "The definition lines in the Nexus file are not correctly formatted. " 313 "Definition lines are optional, " 314 "but if included, must start with \">\" followed by modifiers in square brackets. " 315 "The sequences have been imported " 316 "but the information in the definition lines will be ignored."

;

322 mDeflines

.push_back({defLine, lineNum});

334 auto

lineNum =

command

.front().mNumLine;

335 auto

newBlockName =

command

.front().mData;

338 "Nested blocks detected. New block \"%s\" while still in \"%s\" block. \"%s\" block begins on line %d"

339

newBlockName.c_str(),

363 auto

description =

"\"end\" command appears outside of block."

;

382 int

dataLineCount(0);

384 int

blockLineLength(0);

385 int

sequenceCharCount(0);

388 for

(

auto

lineInfo :

command

) {

389 const auto

data

= lineInfo.mData;

390 const int

lineNum = lineInfo.mNumLine;

392

vector<string> tokens;

394 if

(tokens.size() < 2) {

396 "Data line does not follow the expected pattern of sequence_ID followed by sequence data. " 397 "Each data line should conform to the same expected pattern."

;

404 const string

& seqId = tokens[0];

412

seqCount = inFirstBlock ? dataLineCount : (dataLineCount %

mNumSequences

);

413

maxSeqCount =

max

(seqCount, maxSeqCount);

419 mSeqIds

.push_back({seqId, lineNum});

423 string

seqData =

NStr::Join

(tokens.begin()+1, tokens.end(),

""

);

424 const int

dataSize = seqData.size();

428

sequenceCharCount += dataSize;

432 "The expected number of characters per sequence specified by nChar in the Nexus file is %d. " 433 "The actual number of characters counted for the first sequence is %d. " 434 "The expected number of characters must equal the actual number of characters."

442

blockLineLength = dataSize;

445 if

(dataSize != blockLineLength) {

453 mSequences

[seqCount].push_back({seqData, lineNum});

462 "The expected number of sequences specified by nTax in the Nexus file is %d. " 463 "The actual number of sequences encountered is %d. " 464 "The number of sequences in the file must equal the expected number of sequences."

473 if

(seqCount != maxSeqCount) {

476 "The final sequence block in the Nexus file is incomplete. " 477 "It contains data for just %d sequences, but %d sequences are expected."

488 "The expected number of characters per sequence specified by nChar in the Nexus file is %d. " 489 "The actual number of characters counted for the first sequence is %d. " 490 "The expected number of characters must equal the actual number of characters."

513 if

(ntaxPos.second != string::npos) {

515 size_t

ntaxLinePos = ntaxPos.second;

516 if

(ntaxLinePos == 0 &&

517

ntaxPos.first != args.begin()) {

518

ntaxSubStr =

(ntaxPos.first)->mData;

519

ntaxLinePos += ntaxSubStr.size();

522 bool

foundError =

true

;

523 const auto

litLength = strlen(

"newtaxa"

);

524 if

(ntaxLinePos > litLength) {

525

ntaxSubStr += ntaxPos.first->mData;

526 auto

endOfPreviousToken = ntaxSubStr.find_last_not_of(

" \t"

, ntaxLinePos-1);

527 if

(endOfPreviousToken !=

NPOS

528

endOfPreviousToken >= (litLength-1) &&

531

endOfPreviousToken-(litLength-1), litLength),

"newtaxa"

)) {

538

ntaxPos.first->mNumLine,

540 "Invalid command arguments. \"nTax\" must be immediately preceded by \"newtaxa\" in \""

550 if

(!ntax.first.empty()) {

556 ErrorPrintf

(

"Nexus file has invalid nTax setting: \"%s\". nTax must be an integer."

566 if

(!nchar.first.empty()) {

572 ErrorPrintf

(

"Nexus file has invalid nChar setting: \"%s\". nChar must be an integer."

573

nchar.first.c_str());

593 if

(!missing.first.empty()) {

597 if

(!gap.first.empty()) {

601 if

(!matchchar.first.empty()) {

619 for

(

auto

lineInfo :

command

) {

620 if

(keyPos ==

NPOS

) {

622 if

(keyPos !=

NPOS

) {

623

keyLine = lineInfo.mNumLine;

624

endPos = lineInfo.mData.find_first_of(

" \t="

, keyPos);

628 if

(keyPos !=

NPOS

) {

629 int

currentLine = lineInfo.mNumLine;

630 if

(currentLine != keyLine) {

633

valPos = lineInfo.mData.find_first_not_of(

" \t="

, endPos);

634 if

(valPos !=

NPOS

) {

635

endPos = lineInfo.mData.find_first_of(

" \t\n;"

, valPos);

636 if

(endPos !=

NPOS

) {

637 return

{lineInfo.mData.substr(valPos, endPos-valPos), lineInfo.mNumLine};

639 return

{lineInfo.mData.substr(valPos), lineInfo.mNumLine};

647

pair<CAlnScannerNexus::TCommandArgs::const_iterator, size_t>

649 const string

& token)

const 652 for

(

auto

it = args.cbegin(); it != args.cend(); ++it) {

653 string

line(it->mData);

655 size_t

pos = line.find(token);

656 if

(pos != string::npos) {

657 return

make_pair(it, pos);

661 return

make_pair(args.cend(), string::npos);

670 int

&numUnmatchedLeftBrackets,

674 for

(

auto

index=startPos; index<line.size(); ++index) {

675 if

(line[index] ==

'['

) {

676

++numUnmatchedLeftBrackets;

679 if

(line[index] ==

']'

) {

680

--numUnmatchedLeftBrackets;

683 if

((numUnmatchedLeftBrackets == 0) &&

702 size_t

commandEnd(0);

703 size_t

commandStart(0);

704 int

numOpenBrackets(0);

705 size_t

commentStartLine(-1);

706 bool

inCommand(

false

);

707 bool

firstToken =

true

;

710 while

(iStr.

ReadLine

(line, lineCount)) {

714 string

lineStrLower(line);

716 if

(lineStrLower ==

"#nexus"

) {

721 "Unexpected token. \"#NEXUS\" should appear once at the beginnng of the file." 738 int

previousOpenBrackets = numOpenBrackets;

740 if

(previousOpenBrackets == 0 &&

741

numOpenBrackets > 0) {

742

commentStartLine = lineCount;

749

previousOpenBrackets = numOpenBrackets;

751 if

(previousOpenBrackets == 0 &&

752

numOpenBrackets > 0) {

753

commentStartLine = lineCount;

757 while

(commandEnd !=

NPOS

) {

758 string

commandSubstr =

760 if

(!commandSubstr.empty()) {

761

commandTokens.push_back({commandSubstr, lineCount});

764

commandTokens.clear();

766

commandStart = commandEnd+1;

767

previousOpenBrackets = numOpenBrackets;

770 if

(previousOpenBrackets == 0 &&

771

numOpenBrackets > 0) {

772

commentStartLine = lineCount;

776 if

(commandStart < line.size()) {

783 if

(numOpenBrackets > 0) {

785 "The beginning of a comment was detected, but it is missing a closing bracket. Add the closing bracket to the end of the comment or correct if it is not a comment."

;

792 if

(!commandTokens.empty()) {

794 "Terminating semicolon missing from command. Commands in a Nexus file must end with a semicolon."

;

828 int

&numUnmatchedLeftBrackets)

835

list<pair<size_t, size_t>> commentLimits;

839 while

(index < line.size()) {

840 const auto

& c = line[index];

842

++numUnmatchedLeftBrackets;

843 if

(numUnmatchedLeftBrackets==1) {

849 if

(numUnmatchedLeftBrackets==1) {

851

commentLimits.push_back(make_pair(start, stop));

853

--numUnmatchedLeftBrackets;

858 if

(numUnmatchedLeftBrackets) {

859

commentLimits.push_back(make_pair(start, index-1));

862 for

(

auto

it = commentLimits.crbegin();

863

it != commentLimits.crend();

865

line.erase(it->first, (it->second-it->first)+1);

874 int

&numUnmatchedLeftBrackets,

882

list<pair<size_t,size_t>> commentLimits;

887

(numUnmatchedLeftBrackets == 0) &&

892 const auto len

= line.size();

894 for

(

size_t

index=0; index<

len

; ++index) {

895 const auto

& c = line[index];

899

numUnmatchedLeftBrackets==0) {

907

++numUnmatchedLeftBrackets;

908 if

(numUnmatchedLeftBrackets==1) {

914

--numUnmatchedLeftBrackets;

915 if

(numUnmatchedLeftBrackets==0) {

917

commentLimits.push_back(make_pair(start, stop));

921 if

(numUnmatchedLeftBrackets == 0 &&

927 if

(numUnmatchedLeftBrackets && !inCommand) {

928

commentLimits.push_back(make_pair(start,

len

-1));

931 for

(

auto

it = commentLimits.crbegin();

932

it != commentLimits.crend();

934

line.erase(it->first, (it->second-it->first)+1);

946 int

numUnmatchedLeftBrackets = 0;

950 if

(it->mData.empty()) {

string BadCharCountPrintf(int expectedCount, int actualCount)

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

thread_local unique_ptr< CAlnErrorReporter > theErrorReporter

static void sStripNexusComments(string &line, int &numUnmatchedLeftBrackets)

virtual void xAdjustSequenceInfo(CSequenceInfo &) override

void xProcessTaxaBlockCommand(TCommand &command, CSequenceInfo &sequenceInfo)

static void sStripNexusCommentsFromCommand(TCommandArgs &command)

void xProcessNCBIBlockCommand(TCommand &command, CSequenceInfo &sequenceInfo)

void xProcessFormat(const TCommandArgs &args)

void xProcessDataBlockCommand(TCommand &command, CSequenceInfo &sequenceInfo)

void xEndBlock(int lineNum)

void xProcessMatrix(const TCommandArgs &args)

bool xUnexpectedEndBlock(TCommand &command)

pair< TCommandArgs::const_iterator, size_t > xGetArgPos(const TCommandArgs &args, const string &token) const

void xBeginBlock(const TCommandArgs &command)

TCommand::TArgs TCommandArgs

pair< string, int > xGetKeyVal(const TCommandArgs &command, const string &key)

void xProcessDimensions(const TCommandArgs &args)

TCommandArgs TCommandTokens

static void sStripCommentsOutsideCommand(string &line, int &numUnmatchedLeftBrackets, bool &inCommand)

void xImportAlignmentData(CSequenceInfo &, CLineInput &) override

void xProcessSequin(const TCommandArgs &args)

void xProcessCommand(const TCommandTokens &commandTokens, CSequenceInfo &sequenceInfo)

static size_t sFindCharOutsideComment(char c, const string &line, int &numUnmatchedLeftBrackets, size_t startPos=0)

vector< TLineInfo > mSeqIds

vector< vector< TLineInfo > > mSequences

vector< TLineInfo > mDeflines

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

CSequenceInfo & SetMissing(const string &c)

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.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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 EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

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

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

const struct ncbi::grid::netcache::search::fields::KEY key

@ eAlnSubcode_UnexpectedCommandArgs

@ eAlnSubcode_BadSequenceCount

@ eAlnSubcode_UnterminatedComment

@ eAlnSubcode_UnexpectedCommand

@ eAlnSubcode_IllegalDataDescription

@ eAlnSubcode_UnterminatedCommand

@ eAlnSubcode_IllegalDataLine

@ eAlnSubcode_BadDataCount

@ eAlnSubcode_IllegalDefinitionLine

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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__scanner__nexus_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnscannernexus_8cpp_source.html below: