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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cav__main_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/cddalignview/demo/cav_main.cpp Source File

54

argDescr->

AddKey

(

"type"

"one of: 'text' (unformatted), 'HTML', or 'FASTA'"

, argDescr->

eString

);

58

argDescr->

AddFlag

(

"fasta_lc"

"whether to show unaligned residues in lowercase in FASTA output"

);

65

argDescr->

AddDefaultKey

(

"cons"

"bits"

"conservation threshhold (bit score)"

, argDescr->

eDouble

"2.0"

);

66

argDescr->

AddFlag

(

"identity"

"show identity, ignoring bit score"

);

69

argDescr->

AddFlag

(

"lefttails"

"whether to show left tails"

);

70

argDescr->

AddFlag

(

"righttails"

"whether to show right tails"

);

73

argDescr->

AddFlag

(

"condensed"

"condensed incompletely aligned columns (text/HTML only)"

);

76

argDescr->

AddFlag

(

"no_color_bg"

"don't use colored backgrounds for alignment paragraphs (HTML only)"

);

79

argDescr->

AddFlag

(

"ignore_bad_aln"

"ignore invalid pairwise alignments in input data"

);

95 ERR_POST

(

Error

"Can't open input file "

<< args[

"in"

].AsString());

101 static const int

bufSize = 65536;

103

asnString.resize(bufSize);

104 int

nBytes = 0,

;

105 while

(!(asnIfstream->eof() || asnIfstream->fail() || asnIfstream->bad())) {

106

asnIfstream->read(

buf

, bufSize);

107 n

= asnIfstream->gcount();

108 if

(nBytes+

> (

int

)asnString.size())

109

asnString.resize(asnString.size() + bufSize*4);

110 for

(

=0;

;

++) asnString[nBytes +

] =

buf

[

];

118 if

(args[

"type"

].AsString() ==

"text"

)

120 else if

(args[

"type"

].AsString() ==

"HTML"

)

122 else if

(args[

"type"

].AsString() ==

"FASTA"

)

140 for

(

=5;

<=90;

+=5) feats[0].locations[

/5 - 1] =

- 1;

142

feats[0].

description

"Long description of Feature 1"

;

147 for

(

=3;

<=90;

+=3) feats[1].locations[

/3 - 1] =

- 1;

149

feats[1].

description

"Long description of Feature 2"

;

162 static_cast<const void

>

(asnString.data()),

165

args[

"width"

].AsInteger(),

166

args[

"cons"

].AsDouble(),

167 "Alignment - created from command line"

177 int main

(

int

argc,

const char

* argv[])

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

C interface header for cddalignview as function call.

#define CAV_NO_PARAG_COLOR

#define CAV_IGNORE_BAD_ALN

int CAV_DisplayMultiple(const void *asnDataBlock, int asnSize, unsigned int options, unsigned int paragraphWidth, double conservationThreshhold, const char *title, int nFeatures, const AlignmentFeature *features)

#define CAV_SHOW_IDENTITY

#define CAV_FASTA_LOWERCASE

void Init(void)

Initialize the application.

int Run(void)

Run the application.

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.

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 SetUsageContext(const string &usage_name, const string &usage_description, bool usage_sort_args=false, SIZE_TYPE usage_width=78)

Set extra info to be used by PrintUsage().

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

Add description for mandatory positional argument.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

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

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.

@ eDiag_Info

Informational message.

void Error(CExceptionArgs_Base &args)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

Defines command line argument related classes.

Defines unified interface to application:

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

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

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