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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asn2fasta_8cpp_source.html below:

NCBI C++ ToolKit: src/app/asn2fasta/asn2fasta.cpp Source File

CALLS_UNTIL_CANCELLED = 25;

(0 == ++mNumCalls % 100) {

cerr <<

<< (CALLS_UNTIL_CANCELLED - mNumCalls) <<

;

(mNumCalls > CALLS_UNTIL_CANCELLED);

mNumCalls;

TestCanceler::mNumCalls = 0;

()

;

()

;

unique_ptr<CFastaOstreamEx>

;

unique_ptr<CFastaOstreamEx>

;

unique_ptr<CFastaOstreamEx>

;

unique_ptr<CFastaOstreamEx>

;

unique_ptr<CFastaOstreamEx>

;

unique_ptr<CFastaOstreamEx>

;

arg_desc->SetUsageContext(

,

);

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

,

,

));

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetConstraint(

,

&( *

,

,

,

,

,

) );

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

feat_desc =

;

feat_desc +=

;

feat_desc +=

;

feat_desc +=

;

feat_desc +=

;

feat_desc +=

;

feat_desc +=

;

feat_desc +=

;

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

,

,

,

));

arg_desc->AddOptionalKey(

,

,

,

);

arg_desc->AddOptionalKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

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arg_desc->AddOptionalKey(

,

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arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

(strname.empty()) {

(argname.empty())

;

(! args[argname])

;

}

( !strname.empty() ) {

os = &args[argname].AsOutputFile();

fasta_os->SetAllFlags(

(args[

])

(args[

])

(args[

]) {

( args[

] ) {

gapmode = args[

].AsString();

( gapmode ==

) {

}

( gapmode ==

) {

}

( gapmode ==

) {

}

( gapmode ==

) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

fasta_os->SetWidth( args[

].AsInteger() );

fasta_os.release();

<<

<< endl;

);

( args[

] ) {

( args[

] ) {

seqID = args[

].AsString();

( args[

] ) {

(id_str.empty() || id_str[0] ==

) {

(args[

]) {

ifname = args[

].AsString();

= !ifname.empty() ?

+ ifname :

;

( args[

] ) {

asn_type = args[

].AsString();

(exception& e) {

= args[

] ? &(args[

].AsOutputFile()) :

;

(args[

] && args[

]) {

(

);

og_maxsize = 1000;

(args[

]) {

og_maxsize = args[

].AsInteger();

& s = args[

].AsString();

= args[

].AsString();

= args[

].AsString();

list<string> feat_list;

(feat_list.empty()) {

(

& feat_name : feat_list) {

(feat_name ==

) {

(feat_name ==

) {

(feat_name ==

) {

(feat_name ==

) {

(feat_name ==

) {

(feat_name ==

) {

+feat_name );

.RegisterHandler(

);

( asn_type ==

) {

( asn_type ==

) {

CSeq_entry::GetTypeInfo(), CSeq_submit::GetTypeInfo(),

CBioseq_set::GetTypeInfo(), CBioseq::GetTypeInfo(),

(matching_types.

()) {

);

}

(matching_types.

() > 1) {

);

}

(*matching_types.

() == CSeq_entry::GetTypeInfo()) {

}

(*matching_types.

() == CSeq_submit::GetTypeInfo()) {

}

(*matching_types.

() == CBioseq_set::GetTypeInfo()) {

}

(*matching_types.

() == CBioseq::GetTypeInfo()) {

);

( asn_type ==

) {

( asn_type ==

) {

( asn_type ==

) {

);

);

(

<< seq_id <<

);

is_genomic =

;

is_RNA =

;

(closest_molinfo) {

( bsh.

() ) {

( (is_genomic || ! closest_molinfo) &&

) {

fasta_os =

.get();

fasta_os =

.get();

}

( is_RNA &&

) {

fasta_os =

.get();

( bsh.

() ) {

!(feat_handle.GetData().IsCdregion() ||

feat_handle.GetData().IsGene() ||

feat_handle.GetData().IsRna());

( tseh.

() ) {

.BasicCleanup( *tmp_se );

( tmp_se->

() ) {

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

( !fasta_os )

;

fasta_os->

(bsh);

vector<CSeq_id_Handle> product_ids;

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

( ; feat_it; ++feat_it) {

vector<CBioseq_Handle> product_handles;

( all_nuc_loc ) {

( all_prot_loc ) {

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

( ; feat_it; ++feat_it) {

( args[

] ) {

&

= args[

].AsString();

(

==

) {

}

(

==

) {

}

(

==

) {

bDeleteOnClose =

;

( !ifname.empty() ) {

bDeleteOnClose =

;

( args[

] ) {

ext =

;

ext = args[

].AsString();

=

+ ext;

ifname = de->GetPath();

ofname = ifname;

ofname.resize(ofname.size() - ext.size());

=

+ ifname;

(args[

]) {

asn_type = args[

].AsString();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static const CDataLoadersUtil::TLoaders kDefaultLoaders

#define asn2fasta_app_main

ncbi::TMaskedQueryRegions mask

int x_ProcessISubdirectory(const CDir &)

int Run() override

Run the application.

bool HandleSeqID(const string &seqID)

CRef< CObjectManager > m_Objmgr

CFastaOstreamEx * OpenFastaOstream(const string &argname, const string &strname, bool use_stdout)

CArgValue::TStringArray m_FeatureSelection

void x_ProcessIStream(const string &asn_type, CObjectIStream &istr)

CObjectIStream * x_OpenIStream(const string &ifname)

void Init() override

Initialize the application.

unique_ptr< CFastaOstreamEx > m_Op

unique_ptr< CFastaOstreamEx > m_Or

void x_InitOStreams(const CArgs &args)

void x_BatchProcess(CObjectIStream &istr)

CSeq_entry_Handle ObtainSeqEntryFromSeqEntry(CObjectIStream &is)

void PrintQualityScores(const CBioseq &bioseq, CNcbiOstream &ostream)

unique_ptr< CFastaOstreamEx > m_Ou

unique_ptr< CFastaOstreamEx > m_On

bool x_IsOtherFeat(const CSeq_feat_Handle &feat) const

unique_ptr< CQualScoreWriter > m_pQualScoreWriter

CSeq_entry_Handle ObtainSeqEntryFromBioseqSet(CObjectIStream &is)

unique_ptr< CFastaOstreamEx > m_Og

CFastaOstreamEx * x_GetFastaOstream(CBioseq_Handle &handle)

bool HandleSeqEntry(CRef< CSeq_entry > &se) override

user code for handling a Seq-entry goes here.

CSeq_entry_Handle ObtainSeqEntryFromBioseq(CObjectIStream &is)

void x_InitFeatDisplay(const string &feats)

CSeq_entry_Handle ObtainSeqEntryFromSeqSubmit(CObjectIStream &is)

unique_ptr< CFastaOstreamEx > m_Os

CBioseq_set_EditHandle –.

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

TSeqPos GetLength(void) const

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void AddArgumentDescriptions(CArgDescriptions &arg_desc, TLoaders loaders=fDefault)

Add a standard set of arguments used to configure the object manager.

void WriteFeatureTitle(const CSeq_feat &feat, CScope &scope, bool translate_cds=false)

void WriteFeature(const CSeq_feat &feat, CScope &scope, bool translate_cds=false)

Interface for handling Seq-entry objects.

CGBReleaseFile is a utility class to ease the processing of Genbank release files one Seq-entry at a ...

void SetCanceler(ICanceled *pCanceller)

namespace ncbi::objects::

CZipStreamDecompressor – zlib based decompression stream processor.

Interface for testing cancellation request in a long lasting operation.

const_iterator begin() const

static void cleanup(void)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const string & GetProgramDisplayName(void) const

Get the application's "display" name.

const CVersionAPI & GetFullVersion(void) const

Get the program version information.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

vector< string > TStringArray

Some values types can contain several value lists.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ eDirectory

Name of file directory.

@ fCheckFileHeader

Check (and skip) gzip file header on decompression stage.

#define ERR_FATAL(message)

Posting fatal error and abort.

#define WARNING_POST(message)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

bool CheckAccess(TMode access_mode) const

Check access rights.

virtual bool Exists(void) const

Check if directory "dirname" exists.

string GetName(void) const

Get the base entry name with extension (if any).

@ fIgnoreRecursive

Suppress "self recursive" elements (the directories "." and "..").

C * SerialClone(const C &src)

Create on heap a clone of the source object.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

virtual set< TTypeInfo > GuessDataType(const set< TTypeInfo > &known_types, size_t max_length=16, size_t max_bytes=1024 *1024)

Identify the type of data in the stream.

virtual bool EndOfData(void)

Check if there is still some meaningful data that can be read; in text streams this function will ski...

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

virtual void WriteTitle(const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr)

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

@ fNoExpensiveOps

don't try too hard to find titles

@ fShowModifiers

show key-value pair modifiers (e.g. "[organism=Homo sapiens]")

@ fInstantiateGaps

honor specifed gap mode; on by default

@ fHideGenBankPrefix

Hide gb| prefix for genbank only seq_id's.

@ fKeepGTSigns

don't convert '>' to '_' in title

@ fShowGnlAndAcc

Show general id and accession in the defline.

@ fNoDupCheck

skip check for duplicate sequence IDs

@ fIgnoreOriginalID

Disregard original ID when constructing defline.

@ fEnableGI

Use this flag to enable GI output in the defline.

@ fAssembleParts

assemble FAR delta sequences; on by dflt

@ eGM_letters

Multiple inline Ns or Xs as appropriate (default).

@ eGM_count

>?N or >?unk100, as appropriate.

@ eGM_dashes

Multiple inline dashes.

@ eGM_one_dash

A single dash, followed by a line break.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TBioseqHandles GetBioseqHandles(const TIds &ids)

Get bioseq handles for all ids.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

TBulkIds GetBulkIds(const TSeq_id_Handles &idhs, TGetFlags flags=0)

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TSet SelectSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the empty Seq-entry to Bioseq-set.

CConstRef< TObject > GetCompleteObject(void) const

const CSeqFeatData & GetData(void) const

const CTSE_Handle & GetTSE_Handle(void) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

Remove current seqset-entry from its location.

CConstRef< TObject > GetCompleteObject(void) const

TSeq SelectSeq(CBioseq &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

bool IsProtein(void) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TMol GetSequenceType(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool IsSetData(void) const

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

@ eSortOrder_Normal

default - increasing start, decreasing length

static CRef< CSeqMap > CreateSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

bool CanResolveRange(CScope *scope, const SSeqMapSelector &sel) const

CRef< C > Ref(C *object)

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

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 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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

Convert int to string.

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

Truncate whitespace in a string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eCurrent

Use current time. See also CCurrentTime.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

const SBuildInfo & GetBuildInfo() const

Get build info (date and tag, if set)

CTime GetBuildTime(void) const

Converts 'date' parameter to CTime.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

TSet & SetSet(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if variant Set is selected.

TSeq & SetSeq(void)

Select the variant.

@ e_not_set

No variant selected.

TBiomol GetBiomol(void) const

Get the Biomol member data.

EMol

molecule class in living organism

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Molinfo

info on the molecule and techniques

@ eMol_na

just a nucleic acid

void SetData(TData &value)

Assign a value to Data data member.

const struct ncbi::grid::netcache::search::fields::EXPIRES expires

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

Utility macros and typedefs for exploring NCBI objects from seq.asn.

#define NCBI_BIOMOL(Type)

CMolInfo definitions.

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

Selector used in CSeqMap methods returning iterators.

static wxAcceleratorEntry entries[3]

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