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

TOutputFlags fOutputFlags,

: m_pTemplateBioseq(pTemplateBioseq),

m_fOutputFlags(fOutputFlags)

m_pSubmitBlock.Reset(pSubmitBlock);

( pErrorHandler ) {

m_pErrorHandler = pErrorHandler;

m_pErrorHandler.

(

CErrorHandler );

length = (*ent)->GetSeq().GetInst().GetLength();

((*desc)->IsSource() && (*desc)->GetSource().IsSetSubtype()) {

(*desc)->GetSource().GetSubtype()) {

((*sub_type)->GetSubtype() ==

);

(!chromosomes_istr.eof()) {

list<string> split_line;

(split_line.size() != 2) {

+ line);

= split_line.front();

chr = split_line.back();

(mapChromosomeNames.

(

) != mapChromosomeNames.

()

&& mapChromosomeNames[

] != chr)

+

+

);

mapChromosomeNames[id] = chr;

std::vector<std::string> & vecAgpFileNames,

uMaxBioseqsToWrite )

( ! vecAgpFileNames.empty() ) {

bOnlyOneBioseqInAllAGPFiles =

( agp_entries.size() == 1 && vecAgpFileNames.size() == 1 );

sObjectOpeningString;

sObjectClosingString;

sObjectOpeningString,

sObjectClosingString,

bOnlyOneBioseqInAllAGPFiles );

ostrm << sObjectOpeningString << endl;

bFirstEntry =

;

( std::vector<std::string>, file_name_it, vecAgpFileNames ) {

( ! bFirstEntry ) {

);

bFirstEntry =

;

( bOneObjectPerBioseq ) {

ostrm << sObjectClosingString << endl;

ostrm << sObjectOpeningString << endl;

}

( ! sObjectOpeningString.empty() ) {

ostrm <<

<< endl;

( sObjectOpeningString.empty() ) {

ostrm <<

<< endl;

ostrm <<

<< endl;

obj_writer.

();

ostrm << sObjectClosingString << endl;

& sDirName,

std::vector<std::string> & vecAgpFileNames,

& sSuffix_arg,

outputDir(sDirName);

( ! outputDir.

() ||

! outputDir.

() )

+ sDirName );

& sSuffix = (

sSuffix_arg.empty() ?

( std::vector<std::string>, file_name_it, vecAgpFileNames ) {

);

new_submit->

().SetEntrys().push_back(new_entry);

pObjectToPrint = new_submit;

pObjectToPrint = new_entry;

outputDir.

(), id_str, sSuffix);

( pFileWrittenCallback ) {

pFileWrittenCallback->

(outfpath);

TStrFlagPair kStrFlagPairs[] = {

TStrFlagMap::const_iterator find_iter =

( find_iter == kStrFlagMap.end() ) {

find_iter->second;

TStrErrorPair kStrErrorPairs[] = {

TStrErrorMap::const_iterator find_iter =

( find_iter == kStrErrorMap.end() ) {

find_iter->second;

& sAgpFileName,

stringstream err_strm;

iErrCode = agp_reader.

(istr);

sErrors = err_strm.str();

( ! sErrors.empty() ) {

+ sErrors );

( iErrCode != 0 ) {

+

out_agp_entries.swap( agp_reader.

() );

& out_id_str )

unparsed_id_str;

uAGPBioseqLen = (

( uOrigBioseqLen != uAGPBioseqLen ) {

+ out_id_str +

+

.SetExt().SetDelta().Set()) {

((*delta)->IsLiteral() &&

(*delta)->GetLiteral().GetLength() == 100) {

(*delta)->SetLiteral().SetFuzz().SetLim();

new_entry, out_id_str);

( ! bSuccessfulValidation ) {

+ out_id_str +

);

new_entry, unparsed_id_str);

& out_unparsed_id_str,

& out_id_str )

stringstream id_strm;

out_unparsed_id_str = id_strm.str();

out_id_str = out_unparsed_id_str;

list<CRef<CSeq_id> > ids;

ids.push_back(pSeqId);

+ out_id_str +

);

bFirstWasTransformed =

;

( bWasTransformed && id_it == ids.begin() ) {

bFirstWasTransformed =

;

bFirstWasTransformed )

& id_str)

((*delta)->IsLoc()) {

comp_id_str =

(*delta)->GetLoc().GetInt().GetId().AsFastaString();

+ comp_id_str +

+ id_str +

);

uCompLen = find_iter->second;

to = (*delta)->GetLoc().GetInt().GetTo();

(to >= uCompLen) {

+ comp_id_str +

+ id_str +

& unparsed_id_str )

sub_source->

(chr_find_iter->second);

vector<CRef<CSeqdesc> > source_descs;

((*desc)->IsSource()) {

source_descs.push_back(*desc);

(source_descs.size() != 1) {

);

& source_desc = *source_descs[0];

& out_sObjectOpeningString,

& out_sObjectClosingString,

bOnlyOneBioseqInAllAGPFiles )

out_sObjectOpeningString.clear();

out_sObjectClosingString.clear();

bUsingBioseqSets =

;

bUsingBioseqSets =

;

bUsingBioseqSets =

;

}

( ! bOnlyOneBioseqInAllAGPFiles )

bUsingBioseqSets =

;

stringstream seq_sub_header_strm;

( out_sObjectOpeningString.empty() ) {

seq_sub_header_strm <<

;

seq_sub_header_strm <<

<< endl;

seq_sub_header_strm <<

;

submit_block_writer.

();

seq_sub_header_strm <<

<< endl;

seq_sub_header_strm <<

<< endl;

out_sObjectOpeningString = seq_sub_header_strm.str();

out_sObjectClosingString =

+ out_sObjectClosingString;

bUsingSeqEntry = (

( bUsingSeqEntry ) {

( out_sObjectOpeningString.empty() ) {

out_sObjectOpeningString +=

;

( bUsingBioseqSets ) {

out_sObjectOpeningString +=

;

( bUsingBioseqSets ) {

( out_sObjectOpeningString.empty() ) {

out_sObjectOpeningString +=

;

out_sObjectOpeningString +=

;

out_sObjectClosingString =

+ out_sObjectClosingString;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

#define STRING_AND_VAR_PAIR(_value)

@ eAgpVersion_auto

auto-detect using the first gap line

This gets called after each file is written, so the caller can do useful things like run asnval on ev...

virtual void Notify(const string &file)=0

virtual ~IIdTransformer(void)

TCompLengthMap m_mapComponentLength

void OutputBioseqs(CNcbiOstream &ostrm, const std::vector< std::string > &vecAgpFileNames, TOutputBioseqsFlags fFlags=0, size_t uMaxBioseqsToWrite=std::numeric_limits< size_t >::max()) const

Outputs the result from the AGP file names as ASN.1.

void x_SetUpObjectOpeningAndClosingStrings(string &out_sObjectOpeningString, string &out_sObjectClosingString, TOutputBioseqsFlags fOutputBioseqsFlags, bool bOnlyOneBioseqInAllAGPFiles) const

Each Bioseq written out will have the out_sObjectOpeningString before it and out_sObjectClosingString...

CRef< IIdTransformer > m_pIdTransformer

bool x_VerifyComponents(CConstRef< objects::CSeq_entry > new_entry, const string &id_str) const

@ fOutputBioseqsFlags_OneObjectPerBioseq

If set, each AGP Bioseq is written as its own object.

@ fOutputBioseqsFlags_WrapInSeqEntry

Bioseqs and Bioseq-sets should always be wrapped in a Seq-entry.

@ fOutputBioseqsFlags_DoNOTUnwrapSingularBioseqSets

Specify this if Bioseq-sets with just one Bioseq in them should _NOT_ be unwrapped into a Bioseq.

TChromosomeMap m_mapChromosomeNames

EError

The different kinds of errors that could occur while processing.

@ eError_SuggestUsingFastaIdOption

@ eError_WrongNumberOfSourceDescs

@ eError_ComponentTooShort

@ eError_SubmitBlockIgnoredWhenOneBigBioseqSet

@ eError_EntrySkippedDueToFailedComponentValidation

@ eError_ChromosomeFileBadFormat

@ eError_OutputDirNotFoundOrNotADir

@ eError_ChromosomeIsInconsistent

@ eError_ChromosomeMapIgnoredBecauseChromosomeSubsourceAlreadyInTemplate

@ eError_ComponentNotFound

@ eError_AGPLengthMismatchWithTemplateLength

void SetComponentsBioseqSet(CConstRef< objects::CBioseq_set > pComponentsBioseqSet)

Give a bioseq-set containing all the components pieces, for verification.

CRef< objects::CSeq_entry > x_InitializeCopyOfTemplate(const objects::CBioseq &agp_seq, string &out_unparsed_id_str, string &out_id_str) const

void x_ReadAgpEntries(const string &sAgpFileName, CAgpToSeqEntry::TSeqEntryRefVec &out_agp_entries) const

static TOutputFlags OutputFlagStringToEnum(const string &sEnumAsString)

Convert string to flag.

CAgpConverter(CConstRef< objects::CBioseq > pTemplateBioseq, const objects::CSubmit_block *pSubmitBlock=nullptr, TOutputFlags fOutputFlags=0, CRef< CErrorHandler > pErrorHandler=CRef< CErrorHandler >())

Constructor.

CRef< CErrorHandler > m_pErrorHandler

void OutputOneFileForEach(const string &sDirName, const std::vector< std::string > &vecAgpFileNames, const string &sSuffix=kEmptyStr, IFileWrittenCallback *pFileWrittenCallback=nullptr) const

Outputs the results of each Seq-entry (or Seq-submit if Submit-block was given) into its own file in ...

void x_SetCreateAndUpdateDatesToToday(CRef< objects::CSeq_entry > new_entry) const

void LoadChromosomeMap(CNcbiIstream &chromosomes_istr)

Input has 2 tab-delimited columns: id, then chromosome name.

CConstRef< objects::CBioseq > m_pTemplateBioseq

@ fOutputFlags_Fuzz100

For gaps of length 100, put an Int-fuzz = unk in the literal.

@ fOutputFlags_FastaId

Parse object ids (col. 1) as fasta-style ids if they contain '|'.

@ fOutputFlags_SetGapInfo

Set Seq-gap (gap type and linkage) in delta sequence.

@ fOutputFlags_LAST_PLUS_ONE

@ fOutputFlags_AGPLenMustMatchOrig

When set, we give an error on AGP objects that don't have the same length as the original template.

int TOutputFlags

Bitwise-OR of EOutputFlags.

static EError ErrorStringToEnum(const string &sEnumAsString)

Convert string to EError enum.

void x_SetChromosomeNameInSourceSubtype(CRef< objects::CSeq_entry > new_entry, const string &unparsed_id_str) const

void SetChromosomesInfo(const TChromosomeMap &mapChromosomeNames)

Give the chromosomes to this object.

TOutputFlags m_fOutputFlags

CRef< objects::CSeq_entry > x_InitializeAndCheckCopyOfTemplate(const objects::CBioseq &agp_bioseq, string &out_id_str) const

CConstRef< objects::CSubmit_block > m_pSubmitBlock

Correctly print multiple errors and warnings on consequitive lines; suppress undesired or higly repet...

virtual int ReadStream(CNcbiIstream &is, EFinalize eFinalize=eFinalize_Yes)

Read an AGP file from the given input stream.

This class is used to turn an AGP file into a vector of Seq-entry's.

vector< CRef< objects::CSeq_entry > > TSeqEntryRefVec

This is the way the results will be returned Each Seq-entry contains just one Bioseq,...

@ fSetSeqGap

Found gaps will not be given Seq-data such as Type and Linkage.

TSeqEntryRefVec & GetResult(void)

This gets the results found, but don't call before finalizing.

const CSeq_id * GetFirstId() const

TSeqPos GetLength(void) const

bool IsSetLength(void) const

void SetToTime(const CTime &time, EPrecision prec=ePrecision_second)

ostream & AsString(ostream &s) const

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

virtual bool Exists(void) const

Check if directory "dirname" exists.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

const string & GetPath(void) const

Get entry path.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

@ fLabel_Version

Show the version.

@ fLabel_GeneralDbIsContent

For type general, use the database name as the tag and the (text or numeric) key as the content.

@ eContent

Untagged human-readable accession or the like.

void WriteObject(const CConstObjectInfo &object)

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

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 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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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

Truncate whitespace in a string.

@ fSplit_Tokenize

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

CTime CurrentTime(CTime::ETimeZone tz=CTime::eLocal, CTime::ETimeZonePrecision tzp=CTime::eTZPrecisionDefault)

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

list< CRef< CSubSource > > TSubtype

void SetName(const TName &value)

Assign a value to Name data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

const TLocal & GetLocal(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void ResetId(void)

Reset Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

TSource & SetSource(void)

Select the variant.

const TExt & GetExt(void) const

Get the Ext member data.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

const TDescr & GetDescr(void) const

Get the Descr member data.

TCreate_date & SetCreate_date(void)

Select the variant.

TUpdate_date & SetUpdate_date(void)

Select the variant.

void SetSub(TSub &value)

Assign a value to Sub data member.

void SetData(TData &value)

Assign a value to Data data member.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Int4 delta(size_t dimension_, const Int4 *score_)

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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