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NCBI C++ ToolKit: src/gui/widgets/data/demo/make_score_method.cpp Source File

63

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

64 "Make alignment scoring method files"

);

66

arg_desc->AddDefaultKey(

"out"

"output"

"File name for scoring method"

69

arg_desc->AddOptionalKey(

"sm"

"matrix"

"name of score matrix to use"

71

arg_desc->SetConstraint

73 "blosum45"

"blosum62"

"blosum80"

"pam30"

"pam70"

"pam250"

));

75

arg_desc->AddOptionalKey(

"aa"

"accession"

76 "Amino Acid Index Database accession number"

78

arg_desc->AddDefaultKey(

"in"

"aaindex_file"

79 "Amino Acid Index Database input file."

96 if

(sm ==

"blosum45"

) {

99 " Matrix made by matblas from blosum45.iij\\\n" 100 " BLOSUM Clustered Scoring Matrix in 1/3 Bit Units\\\n" 101 " Blocks Database = /data/blocks_5.0/blocks.dat\\\n" 102 " Cluster Percentage: >= 45\\\n" 103 " Entropy = 0.3795, Expected = -0.2789"

;

104

}

else if

(sm ==

"blosum62"

) {

107 " Matrix made by matblas from blosum62.iij\\\n" 108 " BLOSUM Clustered Scoring Matrix in 1/2 Bit Units\\\n" 109 " Blocks Database = /data/blocks_5.0/blocks.dat\\\n" 110 " Cluster Percentage: >= 62\\\n" 111 " Entropy = 0.6979, Expected = -0.5209"

;

112

}

else if

(sm ==

"blosum80"

) {

115 " Matrix made by matblas from blosum80.iij\\\n" 116 " BLOSUM Clustered Scoring Matrix in 1/2 Bit Units\\\n" 117 " Blocks Database = /data/blocks_5.0/blocks.dat\\\n" 118 " Cluster Percentage: >= 80\\\n" 119 " Entropy = 0.9868, Expected = -0.7442"

;

120

}

else if

(sm ==

"pam30"

) {

123 " This matrix was produced by \\\"pam\\\" Version 1.0.6 [28-Jul-93]\\\n" 124 " PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574\\\n" 125 " Expected score = -5.06, Entropy = 2.57 bits\\\n" 126 " Lowest score = -17, Highest score = 13"

;

127

}

else if

(sm ==

"pam70"

) {

130 " This matrix was produced by \\\"pam\\\" Version 1.0.6 [28-Jul-93]\\\n" 131 " PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574\\\n" 132 " Expected score = -2.77, Entropy = 1.60 bits\\\n" 133 " Lowest score = -11, Highest score = 13"

;

134

}

else if

(sm ==

"pam250"

) {

137 " This matrix was produced by \\\"pam\\\" Version 1.0.7 [01-Feb-98]\\\n" 138 " using Dayhoff et al. (1978) mutability data.\\\n" 139 " PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049\\\n" 140 " Expected score = -0.844, Entropy = 0.354 bits\\\n" 141 " Lowest score = -8, Highest score = 17"

;

146

out_map[

"Name"

] = sm;

147

out_map[

"Builtin"

] = sm;

148

out_map[

"Description"

] = desc.

empty

() ? sm : desc;

157 for

(

int i

= 0;

; ++

) {

159 for

(

int

j = 0; j <

; ++j) {

173 if

( ! out_map[name].

empty

()) {

174 out

<< name <<

" = "

<< out_map[name] << endl;

181 const string

& m_line,

184

out_map[

"Method"

] =

"MatrixScore"

;

191

list<string>::iterator tok_it;

192

tok_it = find(toks.begin(), toks.end(),

"="

);

193 if

(tok_it == toks.end())

196 string

row_bases(*tok_it);

198

tok_it = find(++tok_it, toks.end(),

"="

);

199 if

(tok_it == toks.end())

202 string

col_bases(*tok_it);

205 int

cols = col_bases.size();

206 string

symbols(1, col_bases[0]);

207 for

(

int i

= 1;

< cols; ++

) {

208 char

c = col_bases[

];

209 if

(

isupper

((

unsigned char

) c) || c ==

'-'

) {

214

out_map[

"Columns"

] = symbols;

219 int

rows = row_bases.

size

();

220 for

(

int r

= 0;

< rows; ++

) {

221 if

(! getline(

, line))

223

out_rows += row_bases[

];

228

out_map[

"TableRows"

] = out_rows;

238

out_map[

"Method"

] =

"ColumnScore"

;

248 ITERATE

(list<string>, score_it, scores) {

251

out_rows += *score_it;

255

out_map[

"TableRows"

] = out_rows;

264 while

(getline(

, line)) {

265 if

(line ==

"H "

+ accession)

269

cerr <<

"Accession \""

<< accession <<

"\" not found."

<< endl;

276 while

(getline(

, line)) {

284

current_key =

"Description"

;

285

out_map[current_key] = line;

292

current_key =

"Description"

;

293

out_map[current_key] +=

"\\\n "

+ line;

296 if

( ! current_key.empty()) {

297

out_map[current_key] +=

"\\\n "

+line;

303

current_key.

erase

();

307

cerr <<

"Bad format in M section at accession \"" 308

<< accession <<

"\""

<< endl;

314

cerr <<

"Bad format in I section at accession \"" 315

<< accession <<

"\""

<< endl;

323

cerr <<

"No I or M section at accession \"" 324

<< accession <<

"\""

<< endl;

334 if

(args[

"sm"

] && args[

"aa"

] ) {

335 string msg

"Options -sm and -aa are mutually exclusive.\n"

;

348

out_line[

"Method"

] =

"MatrixScore"

;

349

out_line[

"Type"

] =

"Protein"

;

350

out_line[

"MinimumColor"

] =

"yellow3"

;

351

out_line[

"MaximumColor"

] =

"royal blue"

;

355

}

else if

(args[

"aa"

]) {

356 if

s_ReadAAIndex

(args[

"aa"

].AsString(), args[

"in"

].AsInputFile(), out_line)) {

362 out

"[Info]"

<< endl;

368 out

"[Table]"

<< endl;

378 out

"[TableRows]"

<< endl;

379 out

<< out_line[

"TableRows"

];

int Run(void)

Run the application.

void Init(void)

Initialize the application.

std::ofstream out("events_result.xml")

main entry point for tests

static char line1[1024 *16]

static char line2[1024 *16]

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.

const CArgDescriptions * GetArgDescriptions(void) const

Get argument descriptions (set by SetupArgDescriptions)

const CNcbiArguments & GetArguments(void) const

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

virtual string & PrintUsage(string &str, bool detailed=false) const

Print usage message to end of specified string.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int to string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

static bool sReadAA_I(CNcbiIstream &in, map< string, string > &out_map)

static const string kAAIndexOrder("ARNDCQEGHILKMFPSTWYV")

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

static void s_BuiltInSM(const string &sm, map< string, string > &out_map)

static void sWriteLine(CNcbiOstream &out, map< string, string > &out_map, const string &name)

static bool sReadAA_M(CNcbiIstream &in, const string &m_line, map< string, string > &out_map)

bool s_ReadAAIndex(const string &accession, CNcbiIstream &in, map< string, string > &out_map)

static string s_FormatAA(int aa)

constexpr bool empty(list< Ts... >) noexcept

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Process information in the NCBI Registry, including working with configuration files.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

const SNCBIPackedScoreMatrix NCBISM_Blosum80

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

const TNCBIScore * scores

strlen(symbols) x strlen(symbols)

const char * symbols

order of residues

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/make__score__method_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/data/demo/make_score_method.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/makescoremethod_8cpp_source.html below: