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NCBI C++ ToolKit: src/algo/structure/struct_util/demo/struct_util_demo.cpp Source File

57 #define ERROR_MESSAGE(s) ERR_POST(Error << "struct_util_demo: "

<< s << '!')

58 #define WARNING_MESSAGE(s) ERR_POST(Warning << "struct_util_demo: "

<< s)

59 #define INFO_MESSAGE(s) ERR_POST(Info << "struct_util_demo: "

<< s)

60 #define TRACE_MESSAGE(s) ERR_POST(Trace << "struct_util_demo: "

<< s)

63 template

class

ASNClass >

71

*err =

"Cannot open file for reading"

;

75

unique_ptr<CObjectIStream> inObject;

88

*inObject >> *ASNobject;

89

}

catch

(std::exception& e) {

100 template

class

ASNClass >

101 bool WriteASNToFile

(

const char

*filename,

const

ASNClass& ASNobject,

bool

isBinary,

110

*err =

"Cannot open file for writing"

;

114

unique_ptr<CObjectOStream> outObject;

127

*outObject << ASNobject;

129

}

catch

(std::exception& e) {

145

argDescr->

AddKey

(

"i"

"filename"

"name of input CD"

, argDescr->

eString

);

146

argDescr->

AddKey

(

"o"

"filename"

"name of output CD"

, argDescr->

eString

);

149

argDescr->

AddFlag

(

"ob"

"output binary data"

);

152

argDescr->

AddFlag

(

"IBM"

"do only IBM"

);

155

argDescr->

AddFlag

(

"LOO"

"do leave-one-out"

);

158

argDescr->

AddOptionalKey

(

"f"

"integer"

"first block to realign (post-IBM, from 1)"

, argDescr->

eInteger

);

160

argDescr->

AddOptionalKey

(

"l"

"integer"

"last block to realign (post-IBM, from 1)"

, argDescr->

eInteger

);

162

argDescr->

AddOptionalKey

(

"p"

"double"

"allowed loop length percentile"

, argDescr->

eDouble

);

167

SetupArgDescriptions(argDescr);

175 ERROR_MESSAGE

(

"Cannot open file '"

<< filename <<

"' for reading"

);

179

*inStream >> firstWord;

180 bool

isBinary = !(firstWord ==

"Cdd"

);

225 if

ReadCD

(args[

"i"

].AsString(), &cdd)) {

226 ERROR_MESSAGE

(

"error reading input file "

<< args[

"i"

].AsString());

244 else if

(args[

"LOO"

HasValue

()) {

245

vector < unsigned int > blocksToRealign;

246 for

(

int i

=args[

"f"

].AsInteger();

<=args[

"l"

].AsInteger(); ++

)

247

blocksToRealign.push_back(

- 1);

248 INFO_MESSAGE

(

"score of row "

<< args[

"r"

].AsInteger() <<

" vs. PSSM(N) before realignment: " 252

args[

"r"

].AsInteger() - 1, blocksToRealign,

253

args[

"p"

].AsDouble(), args[

"e"

].AsInteger(), 0))

258 INFO_MESSAGE

(

"score of row "

<< args[

"r"

].AsInteger() <<

" vs PSSM(N) after realignment: " 269 ERROR_MESSAGE

(

"error writing output file "

<< args[

"o"

].AsString());

282 int main

(

int

argc,

const char

* argv[])

const SeqAnnotList & GetSeqAnnots(void)

const BlockMultipleAlignment * GetBlockMultipleAlignment(void)

bool DoLeaveOneOut(unsigned int row, const std::vector< unsigned int > &blocksToRealign, double percentile, unsigned int extension, unsigned int cutoff, unsigned int queryFrom=0, unsigned int queryTo=kMax_UInt)

int ScoreRowByPSSM(unsigned int row)

unsigned int NRows(void) const

CObjectIStreamAsnBinary â.

CObjectOStreamAsnBinary â.

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

main entry point for tests

void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)

Add description for flag argument.

void SetConstraint(const string &name, const CArgAllow *constraint, EConstraintNegate negate=eConstraint)

Set additional user defined constraint on argument value.

void AddKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for mandatory key.

void AddOptionalKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for optional key without default value.

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagPostFlag(EDiagPostFlag flag)

Set the specified flag (globally).

void UnsetDiagTraceFlag(EDiagPostFlag flag)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

void SetDiagTrace(EDiagTrace how, EDiagTrace dflt=eDT_Default)

Set the diagnostic trace settings.

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

Set diagnostic stream.

@ eDPF_File

File name (not full path)

@ eDS_Default

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

@ eDT_Disable

Ignore messages of severity "eDiag_Trace".

@ eDT_Default

Restores the default tracing context.

@ eDiag_Info

Informational message.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

static void SetVerifyDataGlobal(ESerialVerifyData verify)

EFixNonPrint

How to process non-printing character in the ASN VisibleString.

@ eSerialVerifyData_Always

always verify (even if set not to later on)

static void SetVerifyDataGlobal(ESerialVerifyData verify)

Set up default output data verification for streams created by the current process.

static void SetVerifyDataGlobal(ESerialVerifyData verify)

Set up default input data verification for streams created by the current process.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

const TSequences & GetSequences(void) const

Get the Sequences member data.

const TSeqannot & GetSeqannot(void) const

Get the Seqannot member data.

TSeqannot & SetSeqannot(void)

Assign a value to Seqannot data member.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

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

#define row(bind, expected)

static bool ReadCD(const string &filename, CCdd *cdd)

bool WriteASNToFile(const char *filename, const ASNClass &ASNobject, bool isBinary, std::string *err, EFixNonPrint fixNonPrint=eFNP_Default)

static int SumAllRowScores(AlignmentUtility &au)

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

bool ReadASNFromFile(const char *filename, ASNClass *ASNobject, bool isBinary, std::string *err)

#define WARNING_MESSAGE(s)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/struct__util__demo_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/struct_util/demo/struct_util_demo.cpp Source File

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