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

lineNumber =

.GetLineNum();

(lineNumber == -1) {

<<

.GetID() <<

<<

(

.GetCategory()) <<

<<

.GetMsg() <<

);

<<

.GetID() <<

<<

(

.GetCategory()) <<

<<

.GetLineNum() <<

<<

.GetMsg() <<

);

& idString,

= list<CRef<CSeq_id>>;

m_fValidateIds(fValidateIds),

m_IS(is), m_ReadDone(

), m_ReadSucceeded(

),

m_UseNexusInfo(

)

(!fSingleIdValidate) {

[fSingleIdValidate](

list<CRef<CSeq_id>>& ids,

(

& pId : ids) {

fSingleIdValidate(*pId, lineNum, errorReporter);

{EAlphabet::eAlpha_Default,

{EAlphabet::eAlpha_Nucleotide,

},

{EAlphabet::eAlpha_Protein,

},

{EAlphabet::eAlpha_Dna,

},

{EAlphabet::eAlpha_Rna,

},

{EAlphabet::eAlpha_Dna_no_ambiguity,

{EAlphabet::eAlpha_Rna_no_ambiguity,

alphaMap[alphaId];

& seqId,

& message,

TReadFlags readFlags,

ncbi::objects::ILineErrorListener* pErrorListener)

generate_local_ids,

ncbi::objects::ILineErrorListener*

)

& idString = seqIdInfo.

;

);

num_sequences = alignmentInfo.

();

(num_sequences == 0) {

);

(num_sequences == 1) {

);

(

seqIdInfo : alignmentInfo.

) {

.push_back(ids);

numDeflines = alignmentInfo.

();

(numDeflines ==

.size()) {

(

=0;

< numDeflines; ++

) {

,

,

(begin_len <

[row_i].length()) {

string::iterator s =

[row_i].end();

(s !=

[row_i].begin()) {

(

().find(*s) != string::npos) {

(

=0;

<

; ++

) {

, 0);

aln_stop =

[row_i].size();

vector<bool> is_gap; is_gap.resize(

,

);

vector<bool> prev_is_gap; prev_is_gap.resize(

,

);

vector<TSignedSeqPos> next_start; next_start.resize(

, 0);

prev_aln_pos = 0, prev_len = 0;

new_seg =

;

(

aln_pos = 0; aln_pos < aln_stop; aln_pos++) {

(aln_pos >=

[row_i].length()) {

(!is_gap[row_i]) {

is_gap[row_i] =

;

residue =

[row_i].substr(aln_pos, 1);

(!

(row_i, aln_pos, residue)) {

is_gap[row_i] =

;

( !is_gap[row_i] ) {

is_gap[row_i] =

;

lens.push_back(prev_len = aln_pos - prev_aln_pos);

( !prev_is_gap[row_i] ) {

next_start[row_i] += prev_len;

starts.resize(starts_i +

);

starts[starts_i++] = -1;

starts[starts_i++] = next_start[row_i];;

prev_is_gap[row_i] = is_gap[row_i];

prev_aln_pos = aln_pos;

lens.push_back(aln_stop - prev_aln_pos);

((

)lens.size() == numseg);

->Validate(

);

& alphabet,

& seqData,

& alphabet,

& seqData,

& seqId,

seqChars = seqData;

(!missingChars.empty()) {

(seqChars.begin(), seqChars.end(),

[&](

c) { return missingChars.find(c) != string::npos;}),

alphabet.size() >= 2*26) {

posFirstT = seqChars.find_first_of(

);

posFirstU = seqChars.find_first_of(

);

(posFirstT != string::npos && posFirstU != string::npos) {

=

;

& seqData)

pSeqInst->SetMol(mol);

pSeqInst->SetLength(seqData.size());

.SetIupacaa().Set(seqData);

.SetIupacna().Set(seqData);

, 0);

seq_annot->

().SetAlign().push_back(seq_align);

->SetSet().SetAnnot().push_back(seq_annot);

& seq_set =

->SetSet().SetSeq_set();

& seq_str =

[row_i];

& ids = pSubEntry->SetSeq().SetId();

seqId = ids.front()->AsFastaString();

pSubEntry->SetSeq().SetInst(*pSeqInst);

seq_set.push_back(pSubEntry);

(

& pSeqEntry : seq_set) {

(

& pSeqEntry : seq_set) {

pSeqEntry->SetSeq());

(

&

: mods) {

defline = defline_info.

;

idString = pFirstID->AsFastaString();

errorReporter(idString, defline_info.

, pErrorListener);

logInfo = pErrorListener ?

(mod_handler, bioseq, skipped_mods, logInfo, errorReporter);

pDesc->SetTitle() = title;

bioseq.

().Set().push_back(std::move(pDesc));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

thread_local unique_ptr< CAlnErrorReporter > theErrorReporter

static void sReportError(ILineErrorListener *pEC, EDiagSev severity, int code, int subcode, const string &seqId, int lineNumber, const string &message, ILineError::EProblem problemType=ILineError::eProblem_GeneralParsingError)

static CAlnReader::FValidateIds s_GetMultiIdValidate(CAlnReader::FIdValidate fSingleIdValidate)

static void s_AppendMods(const CModHandler::TModList &mods, string &title)

string sAlnErrorToString(const CAlnError &error)

bool ReadAlignmentFile(istream &istr, bool gen_local_ids, bool use_nexus_info, CSequenceInfo &sequence_info, SAlignmentFile &alignmentInfo, ILineErrorListener *pErrorListener=nullptr)

void remove_if(Container &c, Predicate *__pred)

void Report(int lineNumber, EDiagSev severity, EReaderCode subsystem, EAlnSubcode errorCode, const string &descr, const string &seqId="")

CAlnError(int category, int line_num, string id, string message)

EAlnErr GetCategory() const

const string & GetMsg() const

const string & GetID() const

class CAlnReader supports importing a large variety of text-based alignment formats into standard dat...

vector< string > m_IdStrings

void ParseDefline(const string &defline, const SDeflineParseInfo &info, const TIgnoredProblems &ignoredErrors, list< CRef< objects::CSeq_id >> &ids, bool &hasRange, TSeqPos &rangeStart, TSeqPos &rangeEnd, TSeqTitles &seqTitles, objects::ILineErrorListener *pMessageListener)

void x_ParseAndValidateSeqIds(const TLineInfo &seqIdInfo, TReadFlags flags, TIdList &ids)

objects::CFastaDeflineReader::TIgnoredProblems TIgnoredProblems

objects::CSeq_inst::EMol GetSequenceMolType(const string &alphabet, const string &seqData, objects::ILineErrorListener *pErrorListener=nullptr)

Get a sequence's moltype, also considering the alphabet used to read it.

void x_CalculateMiddleSections()

virtual ~CAlnReader(void)

objects::CFastaDeflineReader::SDeflineParseInfo SDeflineParseInfo

void SetPaup(EAlphabet alpha)

vector< string > m_SeqVec

void Read(bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)

TAlignMiddles m_MiddleSections

function< void(const list< CRef< objects::CSeq_id > > &, int, objects::CAlnErrorReporter *)> FValidateIds

static string GetAlphabetLetters(EAlphabet)

vector< TSeqPos > m_SeqLen

objects::CSeq_inst::EMol x_GetSequenceMolType(const string &alphabet, const string &seqData, const string &seqId="", objects::ILineErrorListener *pErrorListener=nullptr)

const string & GetMiddleGap(void) const

int TReadFlags

binary OR of EReadFlags

objects::CDense_seg::TDim TNumrow

const string & GetAlphabet(void) const

pair< TSeqPos, TSeqPos > TAlignMiddleInterval

characters have different contexts, depending on whether they are before the first non-gap character,...

FValidateIds m_fValidateIds

objects::CFastaDeflineReader::TFastaFlags TFastaFlags

CRef< objects::CSeq_inst > x_GetSeqInst(objects::CSeq_inst::EMol mol, const string &seqData) const

void SetClustal(EAlphabet alpha)

void x_AddMods(const TLineInfo &defline_info, objects::CBioseq &bioseq, objects::ILineErrorListener *pErrorListener)

function< void(const objects::CSeq_id &, int, objects::CAlnErrorReporter *)> FIdValidate

ncbi::objects::CSequenceInfo mSequenceInfo

CRef< objects::CSeq_align > GetSeqAlign(TFastaFlags fasta_flags=0, objects::ILineErrorListener *pErrorListener=nullptr)

Create ASN.1 classes from the parsed alignment.

EAlignFormat m_AlignFormat

CNcbiIstream & m_IS

Other internal data.

CRef< objects::CSeq_entry > m_Entry

const string & GetEndGap(void) const

bool x_IsGap(TNumrow row, TSeqPos pos, const string &residue)

const string & GetMissing(void) const

objects::CFastaDeflineReader::TSeqTitles TSeqTitles

void SetPhylip(EAlphabet alpha)

void SetAlphabet(const string &value)

virtual CRef< objects::CSeq_id > GenerateID(const string &fasta_defline, const TSeqPos &line_number, TFastaFlags fasta_flags)

CRef< objects::CSeq_align > m_Aln

void x_VerifyAlignmentInfo(const ncbi::objects::SAlignmentFile &, TReadFlags readFlags)

void x_AssignDensegIds(TFastaFlags fasta_flags, objects::CDense_seg &denseg)

CRef< objects::CSeq_entry > GetSeqEntry(TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)

void SetAllGap(const string &value)

Convenience function for setting beginning, middle, and end gap to the same thing.

void x_AddTitle(const string &defline, objects::CBioseq &bioseq)

list< CRef< objects::CSeq_id > > TIdList

Parsed result data (analogous to SAlignmentFile) Seqs are upper-case strings representing the sequenc...

vector< TLineInfo > m_DeflineInfo

void SetFastaGap(EAlphabet alpha)

Alternative & easy way to choose alphabet, etc.

const string & GetBeginningGap(void) const

CAlnReader(CNcbiIstream &is, FValidateIds fIdValidate=nullptr)

const CSeq_id * GetFirstId() const

CAlnErrorReporter * m_pErrorReporter

CDefaultIdErrorReporter(CAlnErrorReporter *pErrorReporter)

void operator()(EDiagSev severity, int lineNum, const string &idString, CFastaIdValidate::EErrCode, const string &msg)

void operator()(const TIds &ids, int lineNum, CAlnErrorReporter *pErrorReporter)

list< CRef< CSeq_id > > TIds

CFastaIdValidate m_FastaIdValidate

static void ParseDefline(const CTempString &defline, const SDeflineParseInfo &info, const TIgnoredProblems &ignoredErrors, TIds &ids, bool &hasRange, TSeqPos &rangeStart, TSeqPos &rangeEnd, TSeqTitles &seqTitles, ILineErrorListener *pMessageListener)

static ESequenceType SequenceType(const char *str, unsigned length=0, ESTStrictness strictness=eST_Default)

Guess sequence type.

static CLineErrorEx * Create(EProblem eProblem, EDiagSev eSeverity, int code, int subcode, const std::string &strSeqId, unsigned int uLine, const std::string &strErrorMessage=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

static void Apply(const CModHandler &mod_handler, CBioseq &bioseq, TSkippedMods &skipped_mods, FPostMessage fPostMessage=nullptr)

list< CModData > TModList

void AddMods(const TModList &mods, EHandleExisting handle_existing, TModList &rejected_mods, FReportError fReportError=nullptr)

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

static void Apply(const CTempString &title, TModList &mods, string &remainder)

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

vector< string > mSequences

size_t NumDeflines() const

size_t NumSequences() const

vector< TLineInfo > mDeflines

Operators to edit gaps in sequences.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static unsigned int line_num

unsigned int TSeqPos

Type for sequence locations and lengths.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

#define FORMAT(message)

Format message using iostreams library.

@ fAddMods

Parse defline mods and add to SeqEntry.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

EAccessionInfo

For IdentifyAccession (below)

static int BestRank(const CRef< CSeq_id > &id)

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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 SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

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

Truncate whitespace in a string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

TLens & SetLens(void)

Assign a value to Lens data member.

vector< TSignedSeqPos > TStarts

void SetDim(TDim value)

Assign a value to Dim data member.

vector< CRef< CSeq_id > > TIds

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

@ eClass_pop_set

population study

void SetData(TData &value)

Assign a value to Data data member.

EMol

molecule class in living organism

void SetDescr(TDescr &value)

Assign a value to Descr data member.

@ eRepr_raw

continuous sequence

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

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

const struct ncbi::grid::netcache::search::fields::SIZE size

@ eAlnSubcode_BadSequenceCount

@ eAlnSubcode_IllegalSequenceId

@ eAlnSubcode_InconsistentMolType

@ eAlnSubcode_InsufficientDeflineInfo

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

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