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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/compartp_8cpp_source.html below:

NCBI C++ ToolKit: src/app/compart/compartp.cpp Source File

30 virtual void Init

(

void

);

31 virtual int Run

(

void

);

43

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

44 "makes compartments from protein BLAST m8"

);

48

arg_desc->AddDefaultKey(

"ifmt"

"InputFormat"

52

arg_desc->SetConstraint(

"ifmt"

54 "tabular"

"seq-align"

"seq-align-set"

"seq-annot"

));

56

arg_desc->AddFlag(

"hits"

67

ostr << ++last_id <<

'\t'

<< subj <<

'\t'

query

'\t'

;

68

ostr <<

->from+1 <<

'\t'

->to+1 <<

'\t'

<< (

->strand?

'+'

'-'

) <<

'\t'

;

69

ostr <<

->covered_aa <<

'\t'

->score <<

'\n'

;

75 bool

hits,

int

& last_id,

const string

query

const string

& subj)

77

unique_ptr<CCompartmentAccessor<THit> > comps_ptr =

79 if

(comps_ptr.get() ==

NULL

)

95

}

while

(comps.

GetNext

(comphits));

102 return id

.IsGi() ?

id

.AsFastaString() :

id

.GetSeqIdString(

true

);

116 string

ifmt = args[

"ifmt"

].AsString();

117 bool

hits = args[

"hits"

];

125 while

(getline(cin,

buf

)) {

127 if

(hit->GetQueryStrand() ==

false

) {

132 if

(new_q != old_q || new_s != old_s) {

133 DoCompartments

(one_query_subj_pair_hitrefs, compart_options, hits, last_id, old_q, old_s);

135

one_query_subj_pair_hitrefs.clear();

139

one_query_subj_pair_hitrefs.push_back(hit);

142 DoCompartments

(one_query_subj_pair_hitrefs, compart_options, hits, last_id, old_q, old_s);

151 int main

(

int

argc,

const char

* argv[])

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

static void SetupArgDescriptions(CArgDescriptions *argdescr)

bool GetFirst(THitRefs &compartment)

Initialize iteration over the results.

bool GetNext(THitRefs &compartment)

Proceed with iteration over the results.

vector< THitRef > THitRefs

TCompartmentStructs MakeCompartments(const TCompartments &asn_representation, CCompartOptions compart_options)

CSplign::THitRefs THitRefs

vector< SCompartment > TCompartmentStructs

list< CRef< CSeq_annot > > TCompartments

TCompartments FormatAsAsn(CCompartmentAccessor< THit > *comparts_ptr, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)

unique_ptr< CCompartmentAccessor< THit > > CreateCompartmentAccessor(const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)

Selects compartments.

int PdbBadRank(const CRef< CSeq_id > &id)

void PrintCompartments(int &last_id, const string &query, const string &subj, const TCompartmentStructs &compartments, ostream &ostr)

string GetSeqIdString(const CSeq_id &id)

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

void DoCompartments(const CSplign::THitRefs &one_query_subj_pair_hitrefs, const CCompartOptions &compart_options, bool hits, int &last_id, const string &query, const string &subj)

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 CNcbiArguments & GetArguments(void) const

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

@ eString

An arbitrary string.

void SetDiagFilter(EDiagFilter what, const char *filter_str)

Set diagnostic filter.

@ eDiagFilter_All

for all non-FATAL

#define NCBI_THROW(exception_class, err_code, message)

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

static int FastaAARank(const CRef< CSeq_id > &id)

bool IsPdb(void) const

Check if variant Pdb is selected.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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