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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/nmer__repeats_8cpp_source.html below:

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

60  virtual void Init

(

void

);

61  virtual int Run

(

void

);

62  virtual void Exit

(

void

);

78

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

79  "n-mer nucleotide repeat finding program"

);

83

arg_desc->AddPositional

85  "fasta format file to read (\"-\" for stdin)"

,

88

arg_desc->AddDefaultKey

90  "Minimum number of repeat units for a dinucleotide repeat " 91  "(0 to suppress dinucleotide search)"

,

94

arg_desc->AddDefaultKey

95

(

"3"

,

"trinuc_min"

,

96  "Minimum number of repeat units for a trinucleotide repeat " 97  "(0 to suppress trinucleotide search)"

,

100

arg_desc->AddDefaultKey

101

(

"4"

,

"tetranuc_min"

,

102  "Minimum number of repeat units for a tetranucleotide repeat " 103  "(0 to suppress tetranucleotide search)"

,

122

vector<int> minima(5);

123

minima[2] = args[

"2"

].AsInteger();

124

minima[3] = args[

"3"

].AsInteger();

125

minima[4] = args[

"4"

].AsInteger();

135

cout <<

"id\trepeat_unit\tnumber_of_repeats\tfrom\tto"

<< endl;

141

vector<TSeqPos> starts, ends;

149  const string id

= itr->GetFirstId()->AsFastaString();

151  for

(

unsigned int n

= 2;

n

<= 4; ++

n

) {

152  if

(minima[

n

] == 0) {

160  for

(

unsigned int

k = 0; k < starts.size(); k++) {

161  string

rep_unit = seq.substr(starts[k],

n

);

163  if

(rep_unit.find_first_not_of(rep_unit.substr(0, 1), 1)

171  if

(rep_unit[2] == rep_unit[0] &&

172

rep_unit[3] == rep_unit[1]) {

178  int

rep_num = (ends[k] - starts[k] + 1) /

n

;

181

cout <<

id

<<

'\t'

<< rep_unit <<

'\t'

<< rep_num <<

'\t' 182

<< starts[k] + 1 <<

'\t'

<< ends[k] + 1 << endl;

204 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

Base class for reading FASTA sequences.

static void FindNucNmerRepeats(const string &seq, int n, int min_repeats, vector< TSeqPos > &starts, vector< TSeqPos > &ends)

Find all cases of at least min_repeats consecutive occurrences of any n-mer consisting of unambiguous...

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

Simple implementation of ILineReader for i(o)streams.

Template class for iteration on objects of class C (non-medifiable version)

Operators to edit gaps in sequences.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

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 CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideLogfile

Hide log file description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eInputFile

Name of file (must exist and be readable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

CRef< CSeq_entry > ReadSet(int max_seqs=kMax_Int, ILineErrorListener *pMessageListener=nullptr)

Read multiple sequences (by default, as many as are available.)

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

const TIupacna & GetIupacna(void) const

Get the variant data.

@ e_Iupacna

IUPAC 1 letter nuc acid code.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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


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