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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/local__finder_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/gnomon/demo/local_finder.cpp Source File

62

arg_desc->AddKey(

"input"

"FastaFile"

63 "File containing FASTA-format sequence"

66

arg_desc->AddDefaultKey(

"from"

"From"

71

arg_desc->AddDefaultKey(

"to"

"To"

76

arg_desc->AddKey(

"model"

"ModelData"

80

arg_desc->AddOptionalKey(

"align"

"Alignments"

84

arg_desc->AddFlag(

"rep"

"Repeats"

);

98 int

left = myargs[

"from"

].AsInteger();

99 int

right = myargs[

"to"

].AsInteger();

100 bool

repeats = myargs[

"rep"

];

108

masked_regions = fastareader.

SaveMask

();

111 if

(masked_regions) {

114

seq_annot->

SetNameDesc

(

"NCBI-FASTA-Lowercase"

);

115

bioseq.

SetAnnot

().push_back(seq_annot);

120 id

->Assign(

.GetSeq_id());

123

repeat->

SetData

().SetImp().SetKey(

"repeat_region"

);

124

feature_table->push_back(repeat);

145 if

(myargs[

"align"

]) {

146 CNcbiIstream

& alignmentfile = myargs[

"align"

].AsInputFile();

151 while

(alignmentfile >> algn >>

getcontig

(cur_contig)) {

152 if

(cur_contig==our_contig)

153

alignments.push_back(algn);

162

gnomon.

Run

(alignments, repeats,

true

false

, 10.0);

178 int main

(

int

argc,

const char

* argv[])

const CSeq_id * GetFirstId() const

Base class for reading FASTA sequences.

double Run(bool leftwall=true, bool rightwall=true, double mpp=10, SPhyloCSFSlice *pcsf_slice=nullptr)

CRef< objects::CSeq_annot > GetAnnot(const objects::CSeq_id &id)

HMM model parameters just create it and pass to a Gnomon engine.

int Run(void)

Run the application.

void Init(void)

Initialize the application.

void SetNameDesc(const string &name)

namespace ncbi::objects::

Seq-loc iterator class â iterates all intervals from a seq-loc in the correct order.

Operators to edit gaps in sequences.

vector< TResidue > CResidueVec

list< CGeneModel > TGeneModelList

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eInputFile

Name of file (must exist and be readable)

@ eInteger

Convertible into an integer number (int or Int8)

@ eSerial_AsnText

ASN.1 text.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

CRef< CSeq_loc > SaveMask(void)

Directs the *following* call to ReadOneSeq to note the locations of lowercase letters.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

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...

void SetIupacCoding(void)

Set coding to either Iupacaa or Iupacna depending on molecule type.

CRange< TSignedSeqPos > TSignedSeqRange

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

const TSeq & GetSeq(void) const

Get the variant data.

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

list< CRef< CSeq_feat > > TFtable

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

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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