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NCBI C++ ToolKit: src/objtools/variation/process/analyze-shift.cpp Source File

(

);

Exit(

);

ProcessHGVS(

&expression,

scope,

&reader,

&pos_left,

&pos_right,

&is_shifted,

&is_different,

&dleft,

&dright);

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

);

SetupArgDescriptions(arg_desc.release());

vector<CRef<CSeq_annot> > annots;

}

(...) {

;}

(annots.size() != 1)

;

->Assign(*annots.front());

(

->GetData().GetFtable().empty() ||

->GetData().GetFtable().size() != 1)

;

(!

->GetData().GetFtable().front()->IsSetLocation())

;

(

->GetData().GetFtable().front()->GetData().GetVariation().GetData().IsSet())

(CVariation_ref::TData::TSet::TVariations::const_iterator inst =

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetSet().GetVariations().begin();

inst !=

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetSet().GetVariations().end(); ++inst)

((*inst)->IsSetData() && (*inst)->GetData().IsInstance() && (*inst)->IsSetData() && (*inst)->GetData().GetInstance().IsSetType() && (*inst)->GetData().GetInstance().GetType() !=

)

= (*inst)->GetData().GetInstance().GetType();

(

->GetData().GetFtable().front()->GetData().GetVariation().GetData().IsInstance() &&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().IsSetType()

=

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetType();

CSeq_loc &orig_loc =

->SetData().SetFtable().front()->SetLocation();

orig_left = pos_left;

orig_right = pos_right;

(orig_loc.IsInt())

orig_left = orig_loc.GetInt().GetFrom();

orig_right = orig_loc.GetInt().GetTo();

(orig_loc.IsPnt())

orig_left = orig_loc.GetPnt().GetPoint();

orig_right = orig_left;

(orig_left != pos_left || orig_right != pos_right)

is_different =

;

pos = orig_loc.GetInt().GetTo();

(orig_loc.GetInt().IsSetStrand())

pnt.

( orig_loc.GetInt().GetStrand() );

pnt.

().Assign(orig_loc.GetInt().GetId());

orig_loc.SetPnt().Assign(pnt);

CSeq_loc &loc =

->GetData().GetFtable().front()->GetLocation();

(

->GetData().GetFtable().front()->GetData().GetVariation().GetData().IsSet())

(CVariation_ref::TData::TSet::TVariations::const_iterator inst =

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetSet().GetVariations().begin();

inst !=

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetSet().GetVariations().end(); ++inst)

( (*inst)->IsSetData() && (*inst)->GetData().IsInstance() && (*inst)->GetData().GetInstance().IsSetDelta() && (*inst)->GetData().GetInstance().GetDelta().size() == 1 &&

(*inst)->GetData().GetInstance().GetDelta().front()->IsSetSeq() && (*inst)->GetData().GetInstance().GetDelta().front()->GetSeq().IsLiteral() &&

(*inst)->GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().IsSetSeq_data() && (*inst)->GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().GetSeq_data().IsIupacna())

ref = (*inst)->GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().GetSeq_data().GetIupacna().Get();

(

->GetData().GetFtable().front()->GetData().GetVariation().GetData().IsInstance() &&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().IsSetDelta()

&&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().size() == 1

&&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().front()->IsSetSeq()

&&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().front()->GetSeq().IsLiteral()

&&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().IsSetSeq_data()

&&

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().GetSeq_data().IsIupacna())

ref =

->GetData().GetFtable().front()->GetData().GetVariation().GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral().GetSeq_data().GetIupacna().Get();

(ref.empty())

;

pos_left = loc.GetPnt().GetPoint();

pos_right = pos_left;

(loc.IsInt())

pos_left = loc.GetInt().GetFrom();

pos_right = loc.GetInt().GetTo();

(pos_left != orig_left || pos_right != orig_right)

dleft = orig_left - pos_left;

dright = pos_right - orig_right;

(!line_reader.

())

line = *(++line_reader);

vector<string> tokens;

NStr::Tokenize(line,

,tokens);

snp_id = tokens[0];

hgvs = tokens[1];

gi = tokens[2];

start = tokens[3];

stop = tokens[4];

isClinical = tokens[5];

is_shifted =

;

is_different =

;

(ProcessHGVS(hgvs,scope,reader,pos_left,pos_right,is_shifted,is_different,dleft,dright))

ostr <<snp_id<<

<<hgvs<<

<<isClinical<<

<<is_different<<

<<is_shifted<<

;

ostr << dleft<<

<<dright<<

<<pos_left<<

<<pos_right<<

;

ostr << line <<

<<endl;

(

argc,

* argv[])

AnalyzeShiftApp.

(argc, argv);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

int main(int argc, const char *argv[])

Data loader implementation that uses the blast databases.

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

bool ProcessHGVS(string &expression, CRef< CScope > scope, CHgvsReader &reader, int &pos_left, int &pos_right, bool &is_shifted, bool &is_different, int &dleft, int &dright)

virtual int Run()

Run the application.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CRef< CGC_Assembly > GetAssembly(const string &acc, const string &mode)

virtual void ReadSeqAnnots(vector< CRef< CSeq_annot > > &, CNcbiIstream &, ILineErrorListener *=0)

Simple implementation of ILineReader for i(o)streams.

static void NormalizeVariation(CVariation &var, ETargetContext target_ctxt, CScope &scope)

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

User-defined methods of the data storage class.

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.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

void Run(void)

Enter the main loop.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

@ eType_identity

delta=[]

Lightweight interface for getting lines of data with minimal memory copying.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

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

NetCache ICache client specs.

Reader-writer based streams.

C++ I/O stream wrappers to compress/decompress data on-the-fly.

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