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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cpgdemo_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/sequence/demo/cpgdemo.cpp Source File

51 virtual void Init

(

void

);

52 virtual int Run

(

void

);

60

argDescr->AddDefaultKey(

"gc"

"gcContent"

"calibrated organism %GC " 61 "content (ie. human: 50, rat: 48)"

63

argDescr->AddDefaultKey(

"cpg"

"obsexp"

64 "observed / expected CpG percentage"

66

argDescr->AddDefaultKey(

"win"

"window_size"

67 "width of sliding window"

69

argDescr->AddDefaultKey(

"len"

"min_length"

70 "minimum length of an island"

72

argDescr->AddOptionalKey(

"m"

"merge_isles"

73 "merge adjacent islands within the specified " 74 "distance of each other"

79

argDescr->AddOptionalKey(

"a"

"accession"

81

argDescr->AddOptionalKey(

"i"

"infile"

82 "List of accessions"

87

argDescr->SetUsageContext(

GetArguments

().GetProgramBasename(),

88 "Scans sequences for CpG islands; uses algorithm based upon Takai & Jones, 2002. Output sent to stdout.\n"

false

);

97 unsigned int len

.m_Stop -

.m_Start + 1;

98

o <<

.m_Start <<

"\t"

.m_Stop <<

"\t"

99

(double) (

.m_C +

.m_G) /

len

"\t"

100

(double)

.m_CG *

len

/ (

.m_C *

.m_G);

115

cerr <<

"Invalid seq-id: '"

<< acc <<

"': "

<< e.

what

() << endl;

121 if

(!bioseq_handle) {

122

cerr <<

"Bioseq load FAILED."

<< endl;

129

seqString.reserve(sv.

size

());

132 CCpGIslands

cpgIsles(seqString.data(), seqString.length(),

133

args[

"win"

].AsInteger(), args[

"len"

].AsInteger(),

134

args[

"gc"

].AsInteger(), args[

"cpg"

].AsInteger());

140

cout << acc <<

"\t"

<< *

<< endl;

160 if

(localID[0] !=

'>'

) {

166 string

seqString, lineBuff;

168

getline(

infile

, lineBuff);

169 if

(seqString.size() + lineBuff.size() > seqString.capacity())

170

seqString.reserve(seqString.capacity() * 2);

171

seqString += lineBuff;

175 CCpGIslands

cpgIsles(seqString.data(), seqString.length(),

176

args[

"win"

].AsInteger(), args[

"len"

].AsInteger(),

177

args[

"gc"

].AsInteger(), args[

"cpg"

].AsInteger());

184

cout << localID <<

"\t"

<< *

<< endl;

208

cout.setf(ios::fixed, ios::floatfield);

209

cout <<

"# CpG islands. Win:"

<< args[

"win"

].AsInteger()

210

"; Min len:"

<< args[

"len"

].AsInteger() <<

"; Min %GC:" 211

<< args[

"gc"

].AsDouble() <<

"; Min obs/exp CpG: " 212

<< args[

"cpg"

].AsDouble();

214

cout <<

"; Merge islands within: "

<< args[

"m"

].AsInteger();

217

cout <<

"# label\tisle_start\tisle_stop\t%GC\tobs/exp CpG"

<< endl;

220

retCode =

ScanForCpGs

(args[

"a"

].AsString(), scope, args);

224

istream &

infile

= args[

"i"

].AsInputFile();

229

cerr <<

"Processing "

<< acc << endl;

237 for

(

unsigned int i

= 1;

<= args.

GetNExtra

(); ++

) {

247 int main

(

int

argc,

char

** argv)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

list< SCpGIsland > TIsles

void MergeIslesWithin(unsigned int range)

const TIsles & GetIsles(void) const

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

int ScanForCpGs(const string &acc, CScope &scope, const CArgs &args)

int main(int argc, char **argv)

CNcbiOstream & operator<<(CNcbiOstream &o, SCpGIsland i)

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.

void DisableArgDescriptions(TDisableArgDesc disable=fDisableStdArgs)

const CNcbiArguments & GetArguments(void) const

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

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

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

@ eDS_Default

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

void Critical(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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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