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__reader_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/readers/aln_reader.hpp Source File

&

()

{

m_ID; }

&

()

{

m_Message; }

objects::CAlnErrorReporter*)>;

<void(

objects::CSeq_id&,

objects::CAlnErrorReporter*)>;

& GetAlphabet(

)

;

SetAlphabet(

&

);

IsAlphabet(

alpha)

;

& GetBeginningGap(

)

;

SetBeginningGap(

&

);

& GetMiddleGap(

)

;

SetMiddleGap(

&

);

& GetEndGap(

)

;

SetEndGap(

&

);

SetAllGap(

&

);

&

(

)

{

mSequenceInfo.Missing();};

&

(

)

{

mSequenceInfo.Match();};

SetFastaGap(EAlphabet alpha);

SetClustal (EAlphabet alpha);

SetPhylip (EAlphabet alpha);

SetPaup (EAlphabet alpha);

fGenerateLocalIDs = 1

generate_local_ids=

,

objects::ILineErrorListener* pErrorListener=

);

objects::ILineErrorListener* pErrorListener=

);

vector<string>&

(

)

{

m_IdStrings;};

vector<string>&

(

)

{

m_Seqs;};

vector<string>&

(

)

{

m_Deflines;};

vector<TLineInfo>&

(

)

{

m_DeflineInfo; };

(

)

{

m_Dim;};

objects::ILineErrorListener* pErrorListener=

);

objects::ILineErrorListener* pErrorListener=

);

objects::CSeq_inst::EMol GetSequenceMolType(

& alphabet,

& seqData,

objects::ILineErrorListener* pErrorListener=

repeat_interval)

;

x_VerifyAlignmentInfo(

& seqData)

;

objects::CSeq_inst::EMol x_GetSequenceMolType(

& alphabet,

& seqData,

& seqId=

,

objects::ILineErrorListener* pErrorListener=

);

x_CalculateMiddleSections();

x_AssignDensegIds(

objects::CDense_seg& denseg);

x_ParseAndValidateSeqIds(

x_AddMods(

& defline_info,

objects::CBioseq& bioseq,

objects::ILineErrorListener* pErrorListener);

x_AddTitle(

& defline, objects::CBioseq& bioseq);

ParseDefline(

& defline,

objects::ILineErrorListener* pMessageListener);

struct SLineInfo SLineInfo

struct SAlignmentFile SAlignmentFile

EAlnErr GetCategory() const

const string & GetMsg() const

const string & GetID() const

const string & GetMessage() const

const_iterator end(void) const

TErrors::const_iterator const_iterator

void push_back(const CAlnError &)

size_t GetErrorCount(CAlnError::EAlnErr) const

list< CAlnError > TErrors

const_iterator begin(void) const

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

vector< string > m_IdStrings

EAlignFormat GetLastAlignmentFileFormat(void) const

const vector< TLineInfo > & GetDeflineInfo(void) const

@ eAlpha_Rna_no_ambiguity

@ eAlpha_Dna_no_ambiguity

objects::CFastaDeflineReader::TIgnoredProblems TIgnoredProblems

const TErrorList & GetErrorList(void) const

int x_GetGCD(const int a, const int b) const

const vector< string > & GetSeqs(void) const

objects::CFastaDeflineReader::SDeflineParseInfo SDeflineParseInfo

bool x_IsReplicatedSequence(const char *sequence_data, int sequence_length, int repeat_interval) const

CAlnReader & operator=(const CAlnReader &value)

void SetUseNexusInfo(bool useNexusInfo)

void Read(TReadFlags=fReadDefaults, objects::ILineErrorListener *pErrorListener=nullptr)

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

const string & GetMiddleGap(void) const

vector< string > m_Deflines

void SetMatch(const string &value)

int TReadFlags

binary OR of EReadFlags

objects::CDense_seg::TDim TNumrow

vector< string > m_Organisms

EReadFlags

Read the file This are the main functions.

const string & GetAlphabet(void) const

pair< TSeqPos, TSeqPos > TAlignMiddleInterval

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

objects::CFastaDeflineReader::TFastaFlags TFastaFlags

bool GetUseNexusInfo() const

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

const vector< string > & GetDeflines(void) const

ncbi::objects::CSequenceInfo mSequenceInfo

const vector< string > & GetIds(void) const

Parsed result data accessors.

objects::CFastaDeflineReader::SLineTextAndLoc SLineTextAndLoc

EAlignFormat m_AlignFormat

const vector< string > & GetOrganisms(void) const

void SetMiddleGap(const string &value)

bool IsAlphabet(EAlphabet alpha) const

objects::CFastaIdHandler m_FastaIdHandler

CNcbiIstream & m_IS

Other internal data.

objects::SLineInfo TLineInfo

CRef< objects::CSeq_entry > m_Entry

const string & GetEndGap(void) const

void SetEndGap(const string &value)

void SetBeginningGap(const string &value)

CAlnReader(const CAlnReader &value)

Prohibit copy constructor and assignment operator.

const string & GetMissing(void) const

const string & GetMatch(void) const

objects::CFastaDeflineReader::TSeqTitles TSeqTitles

void SetAlphabet(const string &value)

CRef< objects::CSeq_align > m_Aln

void SetMissing(const string &value)

void SetAllGap(const string &value)

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

list< CRef< objects::CSeq_id > > TIdList

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

vector< TLineInfo > m_DeflineInfo

vector< TAlignMiddleInterval > TAlignMiddles

const string & GetBeginningGap(void) const

CAlnErrorContainer TErrorList

Include a standard set of the NCBI C++ Toolkit most basic headers.

Operators to edit gaps in sequences.

static unsigned int line_num

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_XOBJREAD_EXPORT

const GenericPointer< typename T::ValueType > T2 value

#define row(bind, expected)

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