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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asn__cleanup_8cpp_source.html below:

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

()

;

(

& filename,

& dir =

,

remove_orig_dir =

);

arg_desc->SetUsageContext(

,

);

arg_desc->SetConstraint(

, &(*

,

,

,

,

));

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetDependency(

,

arg_desc->AddFlag(

,

);

(

c : opt) {

(c !=

&& c !=

&& c !=

&& c !=

&& c !=

) {

(! unrecognized.empty()) {

(

c : opt) {

(c !=

&& c !=

&& c !=

&& c !=

) {

(! unrecognized.empty()) {

(

c : opt) {

(c !=

&& c !=

&& c !=

&& c !=

&&

c !=

&& c !=

&& c !=

) {

(! unrecognized.empty()) {

(args[

])

cfg.

(

,

,

);

(args[

]) {

cerr <<

<< endl;

(args[

]) {

cerr <<

<< endl;

(args[

]) {

(args[

] && (

(args[

].AsString(),

) !=

)) {

(args[

] &&

(args[

].AsString(),

) !=

) {

huge_process.OpenFile(filename);

asn_type = huge_process.GetFile().m_content;

=

+ filename +

;

opened_output =

;

(! args[

] && args[

]) {

opened_output =

;

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

}

(args[

]) {

huge_process.OpenReader();

huge_process.OpenReader();

unique_ptr<CObjectIStream> is = huge_process.GetFile().MakeObjStream(0);

proceed =

;

reader = process.GetReader();

anytop = reader.ReadAny();

(anytop->GetThisTypeInfo() == CSeq_entry::GetTypeInfo()) {

topobject = topentry;

}

(anytop->GetThisTypeInfo() == CSeq_submit::GetTypeInfo()) {

(submit->IsEntrys()) {

topentry = submit->SetData().SetEntrys().front();

(submit->IsSetSub()) {

submit->SetData().SetEntrys().clear();

submit->SetData().SetEntrys().push_back(topentry);

}

(anytop->GetThisTypeInfo() == CBioseq_set::GetTypeInfo()) {

topentry->

(*bioset);

(topentry->

())

}

(anytop->GetThisTypeInfo() == CBioseq::GetTypeInfo()) {

topentry->

(*bioseq);

(topentry->

())

(reader.GetTopEntry()) {

topentry->

(*reader.GetTopEntry());

(reader.GetSubmitBlock()) {

submit->

().Assign(*reader.GetSubmitBlock());

submit->

().SetEntrys().clear();

submit->

().SetEntrys().push_back(topentry);

topobject = topentry;

proceed = process.ForEachEntry(

HandleSeqEntry(seh.GetEditHandle());

writer.PushNextEntry(seh.GetCompleteSeq_entry());

process.ForEachBlob([

](edit::CHugeFileProcess& p_process) ->

{

& reader = p_process.GetReader();

multi_seq = reader.IsMultiSequence();

(multi_seq && !reader.HasLoneProteins()) {

if (reader.HasNestedGenbankSets()) {

m_state.m_changes.SetChanged(CCleanupChange::eCollapseSet);

->ResetLocalHooks();

(topobject->GetThisTypeInfo() == CBioseq::GetTypeInfo()) {

topentry.

(*bioseq);

}

(topobject->GetThisTypeInfo() == CBioseq_set::GetTypeInfo()) {

topentry.

(*bioset);

*

<< *topobject;

*

<< *topobject;

=

+ suffix;

num_files = 0;

(num_files == 0) {

(args[

] && args[

]) {

(

, eInvalidArg,

);

(args[

]) {

(

(args[

].AsString(),

) != string::npos) {

(

(args[

].AsString(),

) != string::npos) {

}

(args[

]) {

(

(args[

].AsString(),

) != string::npos) {

}

(args[

]) {

(args[

]) {

}

(! args[

]) {

.reset(

edit::CTaxonomyUpdater(

));

opened_output =

;

fname = args[

].AsString();

(args[

]) {

(

);

args[

] ? args[

].AsString() :

,

opened_output =

;

}

(! args[

] || args[

]) {

opened_output =

;

seqID = args[

].AsString();

}

(args[

]) {

fname = args[

].AsString();

(args[

]) {

}

(args[

]) {

cerr <<

<< endl;

(

<< seq_id <<

);

(

<< seq_id <<

);

any_changes =

;

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

any_change =

;

(deleted_feats.

()) {

(

: deleted_feats) {

(

orph : orphans) {

any_changes =

;

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(change_defline) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

(

(opt,

) != string::npos) {

cout << e.

() << endl;

cout << e.

() << endl;

any_changes =

;

feat_change =

;

new_mrna->

(*mrna);

new_gene->

(*gene);

changes =

.BasicCleanup(seh, options);

any_changes |= (! changes.Empty());

changes =

.ExtendedCleanup(seh, options);

any_changes |= (! changes.Empty());

any_changes |=

(seh, 0,

);

any_changes =

;

changes = *

.BasicCleanup(entry, options);

any_changes = ! changes.

();

changes = *

.ExtendedCleanup(entry, options);

any_changes = ! changes.

();

any_changes =

;

changes = *

.BasicCleanup(block);

any_changes =

(

, changes);

(args[

]) {

(args[

]) {

any_changes =

;

validator::CTaxValidationAndCleanup tval(

->GetUpdateFunc());

any_changes |= tval.DoTaxonomyUpdate(entry,

);

(args[

] &&

(args[

].AsString(),

) != string::npos) {

(args[

]) {

(! entryHandle) {

(entryHandle.GetCompleteSeq_entry().GetPointer() != se.

()) {

se->

(*entryHandle.GetCompleteSeq_entry());

(args[

]) {

(args[

].AsString() ==

) {

}

(args[

].AsString() ==

) {

}

(args[

].AsString() ==

) {

base = filename;

(remove_orig_dir) {

(pos != string::npos) {

base = base.substr(pos + 1);

any_changes =

;

(changes_str.empty()) {

(

it : changes_str) {

any_changes =

;

list<string> split_args;

vector<const char*> new_argv;

(argc == 2 && argv && argv[1] && strchr(argv[1],

)) {

argc = 1 +

(split_args.size());

new_argv.reserve(argc);

new_argv.push_back(argv[0]);

(

& s : split_args) {

new_argv.push_back(s.c_str());

std::cerr << s.c_str() <<

;

argv = new_argv.data();

(

= 1;

< argc; ++

) {

string_view

{ argv[

] };

(

==

sv) {

(((

+ 1) < argc) && argv[

+ 1]) {

string_view param{ argv[

+ 1] };

(! param.empty() && param[0] !=

) {

argv[

] =

;

cerr <<

;

}

(

==

sv) {

argv[

] =

;

cerr <<

}

(

==

sv) {

cerr <<

;

}

(

==

sv) {

argv[

] =

;

cerr <<

static bool s_IsHugeMode(const CArgs &args, const CNcbiRegistry &cfg)

static const CDataLoadersUtil::TLoaders default_loaders

#define asn_cleanup_app_main

ncbi::TMaskedQueryRegions mask

static bool RegenerateDefLines(CSeq_entry_Handle se)

void x_ProcessOneFile(const string &filename)

bool HandleSeqID(const string &seqID)

bool HandleSubmitBlock(CSubmit_block &block)

void x_FeatureOptionsValid(const string &opt)

unique_ptr< edit::CTaxonomyUpdater > m_tax_updater

const Uint4 kGFF3CDSFixOptions

void x_ProcessOneDirectory(const string &dirname, const string &suffix)

bool HandleSeqEntry(CRef< CSeq_entry > &se)

unique_ptr< CObjectOStream > m_Out

bool x_ProcessHugeFile(edit::CHugeFileProcess &process)

bool x_ProcessFeatureOptions(const string &opt, CSeq_entry_Handle seh)

bool x_RemoveDuplicateFeatures(CSeq_entry_Handle seh)

void x_ProcessBatch(unique_ptr< CObjectIStream > &is)

int Run() override

Run the application.

bool x_ReportChanges(const string_view prefix, CCleanupChangeCore changes)

void x_OpenOStream(const string &filename, const string &dir=kEmptyStr, bool remove_orig_dir=true)

bool x_ProcessXOptions(const string &opt, CSeq_entry_Handle seh, Uint4 options)

void x_KOptionsValid(const string &opt)

bool x_BasicAndExtended(CSeq_entry_Handle entry, const string &label, Uint4 options=0)

bool x_FixCDS(CSeq_entry_Handle seh, Uint4 options, const string &missing_prot_name)

bool x_ProcessHugeFileBlob(edit::CHugeFileProcess &process)

void x_XOptionsValid(const string &opt)

void Init() override

Initialize the application.

bool x_BatchExtendCDS(CSeq_feat &, CBioseq_Handle)

CRef< CSerialObject > x_ProcessTraditionally(edit::CHugeAsnReader &reader)

bool x_GFF3Batch(CSeq_entry_Handle seh)

CRef< CObjectManager > m_Objmgr

All the changes made during cleanup.

vector< string_view > GetDescriptions() const

static bool ConvertDeltaSeqToRaw(CSeq_entry_Handle seh, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set)

static bool RenormalizeNucProtSets(CSeq_entry_Handle seh)

Convert nuc-prot sets with just one sequence to just the sequence can't be done during the explore ph...

static void SetProteinName(CProt_ref &prot, const string &protein_name, bool append)

static bool FixECNumbers(CSeq_entry_Handle entry)

Fix EC numbers.

static size_t MakeSmallGenomeSet(CSeq_entry_Handle entry)

static bool ClearInternalPartials(CSeq_loc &loc, bool is_first=true, bool is_last=true)

Clear internal partials.

static bool WGSCleanup(CSeq_entry_Handle entry, bool instantiate_missing_proteins=true, Uint4 options=0, bool run_extended_cleanup=true, bool also_fix_location=true)

Performs WGS specific cleanup.

static bool ExtendStopPosition(CSeq_feat &f, const CSeq_feat *cdregion, size_t extension=0)

@ eClean_KeepSingleSeqSet

@ eClean_NoNcbiUserObjects

static bool ExtendToStopCodon(CSeq_feat &f, CBioseq_Handle bsh, size_t limit)

Extends a feature up to limit nt to a stop codon, or to the end of the sequence if limit == 0 (partia...

static const string & GetProteinName(const CProt_ref &prot)

static bool SetFrameFromLoc(CCdregion &cdregion, const CSeq_loc &loc, CScope &scope)

Chooses best frame based on location 1.

static bool NormalizeDescriptorOrder(CSeq_descr &descr)

Normalize Descriptor Order on a specific Seq-entry.

static bool LocationMayBeExtendedToMatch(const CSeq_loc &orig, const CSeq_loc &improved)

Checks whether it is possible to extend the original location up to improved one.

static bool RemoveNcbiCleanupObject(CSeq_descr &descr)

Removes NcbiCleanup User Objects in the Seq-descr.

static bool SetGeneticCodes(CBioseq_Handle bsh)

Sets genetic codes for coding regions on Bioseq-Handle.

static bool RemoveUnnecessaryGeneXrefs(CSeq_feat &f, CScope &scope)

Removes unnecessary Gene-xrefs.

static bool MakeIRDFeatsFromSourceXrefs(CSeq_entry_Handle entry)

From SQD-4329 For each sequence with a source that has an IRD db_xref, create a misc_feature across t...

static void AutodefId(CSeq_entry_Handle seh)

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.

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

void StartWriter(CConstRef< CSerialObject > topobject)

SeqMap related exceptions.

SeqVector related exceptions.

void GetLabel(string *label, ELabelType type) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

set< CBioseq_Handle > ListOrphanProteins(CSeq_entry_Handle seh, bool force_refseq=false)

set< CSeq_feat_Handle > GetDuplicateFeaturesForRemoval(CSeq_entry_Handle seh)

static void cleanup(void)

const CNcbiRegistry & GetConfig(void) const

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

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.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ fHidden

Hide it in Usage.

@ 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)

@ eDirectory

Name of file directory.

#define ERR_FATAL(message)

Posting fatal error and abort.

#define ERR_POST(message)

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

Get directory entries based on the specified "mask".

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

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

Assemble a path from basic components.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

bool RetranslateCDS(const CSeq_feat &cds, CScope &scope)

RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current tr...

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

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.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

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

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

void Remove(void) const

Remove the feature from Seq-annot.

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

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

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.

@ fSplit_CanEscape

Allow \... escaping.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eReverseSearch

Search in a backward direction.

@ eCase

Case sensitive compare.

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...

static const char label[]

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

TSet & SetSet(void)

Select the variant.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

void SetClass(TClass value)

Assign a value to Class data member.

virtual void Reset(void)

Reset the whole object.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_genbank

converted genbank

virtual void Reset(void)

Reset the whole object.

@ eMol_na

just a nucleic acid

void SetSub(TSub &value)

Assign a value to Sub data member.

void SetData(TData &value)

Assign a value to Data data member.

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

#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_)

double df(double x_, const double &y_)

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

CCleanupChangeCore m_changes

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