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

52 "Demo application using xalgoalign library"

);

54

argdescr->AddDefaultKey

55

(

"matrix"

"scoring matrix"

60 "the first input sequence in fasta file"

64 "the second input sequence in fasta file"

67

argdescr->AddDefaultKey

69 "End-space free alignment. Format: lrLR where each character " 70 "can be z (free end) or x (regular end) representing " 71 "left and right ends. First sequence's ends are specified first."

75

argdescr->AddDefaultKey

77 "gap preference: earlier or later"

81

argdescr->AddDefaultKey

82

(

"Wm"

"match"

"match bonus (nucleotide sequences)"

86

argdescr->AddDefaultKey

87

(

"Wms"

"mismatch"

"mismatch penalty (nucleotide sequences)"

91

argdescr->AddDefaultKey

92

(

"Wg"

"gap"

"gap opening penalty"

96

argdescr->AddDefaultKey

97

(

"Ws"

"space"

"gap extension (space) penalty"

101

argdescr->AddDefaultKey

102

(

"band"

"Band width in banded alignment"

105

argdescr->AddDefaultKey

106

(

"shift"

107 "Band shift in banded alignment " 108 "(specify negative value to indicate second sequence)"

111

argdescr->AddFlag(

"sw"

112 "run local alignment (Smith-Waterman)"

);

114

argdescr->AddFlag(

"mm"

115 "Use linear-memory alignment algorithm (Myers & Miller)"

);

117

argdescr->AddFlag(

"mt"

"Use multiple threads"

);

120

argdescr->AddOptionalKey

123

argdescr->AddOptionalKey

126

argdescr->AddOptionalKey

127

(

"ofasta"

128 "Generate gapped FastA output for the aligner sequences"

131

argdescr->AddOptionalKey

135

paa_st->

Allow

(

"nucl"

)->

Allow

(

"blosum62"

);

136

argdescr->SetConstraint(

"matrix"

, paa_st);

143

argdescr->SetConstraint(

"esf"

, paa_esf);

146

paa_gp->

Allow

(

"earlier"

)->

Allow

(

"later"

);

147

argdescr->SetConstraint(

"gp"

, paa_gp);

162

unique_ptr<ofstream> pofs0 (

new

ofstream (filename.c_str()) );

169 "Cannot write to file"

+ filename);

179 const bool

bMM = args[

"mm"

];

180 const bool

bMT = args[

"mt"

];

182 bool

output_type1 ( args[

"o1"

] );

183 bool

output_type2 ( args[

"o2"

] );

184 bool

output_asn ( args[

"oasn"

] );

185 bool

output_fasta ( args[

"ofasta"

] );

187 int

band (args[

"band"

].AsInteger());

188 int

shift(args[

"shift"

].AsInteger());

192

eInconsistentParameters,

193 "Mutliple thread mode supported " 194 "for Myers-Miller method only (invoke with -mm)"

);

197 if

(bMM && band >= 0) {

199

eInconsistentParameters,

200 "-mm and -band are inconsistent with each other"

);

207 "This application was built without multithreading support. " 208 "To run in multiple threads, please re-configure and rebuild" 209 " with proper options."

);

215

vector<char> v1,

;

226

pnwaligner =

new CMMAligner

(&v1[0], v1.size(), &

[0],

.size(), psm);

229

pnwaligner =

new CNWAligner

(&v1[0], v1.size(), &

[0],

.size(), psm);

234 Uint1

where = shift >= 0? 0: 1;

239

unique_ptr<CNWAligner> aligner (pnwaligner);

242

aligner->SetWm (args[

"Wm"

]. AsInteger());

243

aligner->SetWms (args[

"Wms"

].AsInteger());

244

aligner->SetScoreMatrix(

NULL

);

246

aligner->SetWg (args[

"Wg"

]. AsInteger());

247

aligner->SetWs (args[

"Ws"

]. AsInteger());

249

aligner->SetScoreMatrix(psm);

254

pmma -> EnableMultipleThreads();

257

unique_ptr<ofstream> pofs1;

258

unique_ptr<ofstream> pofs2;

259

unique_ptr<ofstream> pofsAsn;

260

unique_ptr<ofstream> pofsFastA;

263

pofs1.reset(

open_ofstream

(args[

"o1"

].AsString()).release());

267

pofs2.reset(

open_ofstream

(args[

"o2"

].AsString()).release());

271

pofsAsn.reset(

open_ofstream

(args[

"oasn"

].AsString()).release());

275

pofsFastA.reset(

open_ofstream

(args[

"ofasta"

].AsString()).release());

279 string

ends = args[

"esf"

].AsString();

280 bool

L1 = ends[0] ==

'z'

;

281 bool

R1 = ends[1] ==

'z'

;

282 bool

L2 = ends[2] ==

'z'

;

283 bool

R2 = ends[3] ==

'z'

;

284

aligner->SetEndSpaceFree(L1, R1, L2, R2);

287

aligner->SetSmithWaterman(args[

"sw"

]);

289 if

( args[

"gp"

].AsString() ==

"earlier"

) {

291

}

else if

(args[

"gp"

].AsString() ==

"later"

) {

297 int

score = aligner->Run();

298

cerr <<

"Score = "

<< score << endl;

303 const size_t

line_width = 100;

320 if

(pofsFastA.get()) {

325 if

(!output_type1 && !output_type2

326

&& !output_asn && !output_fasta)

341

vector<char>* sequence)

const 343

vector<char>& vOut = *sequence;

346

ifstream ifs(filename.c_str());

352 if

(

str

[0] ==

'>'

) {

368 copy

(s.begin(), s.end(), back_inserter(vOut));

380 int main

(

int

argc,

const char

* argv[])

virtual int Run()

Run the application.

CRef< objects::CSeq_id > x_ReadFastaFile(const string &filename, vector< char > *sequence) const

virtual void Exit()

Cleanup on application exit.

virtual void Init()

Initialize the application.

static const char * str(char *buf, int n)

void AsText(string *output, ETextFormatType type, size_t line_width=100) const

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

static TScore GetDefaultWg(void)

static TScore GetDefaultWms(void)

static TScore GetDefaultWs(void)

void SetShift(Uint1 where, size_t offset)

static TScore GetDefaultWm(void)

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.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

@ eDS_Default

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

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Reset(void)

Reset reference object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToUpper(string &str)

Convert string to upper case â string& version.

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

unique_ptr< ofstream > open_ofstream(const string &filename)

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

const SNCBIPackedScoreMatrix NCBISM_Blosum62

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