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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/analyze_8cpp_source.html below:

NCBI C++ ToolKit: src/app/read_blast_result/analyze.cpp Source File

67 bool

in_pool_prot,

bool

against_prot)

69 if

(

PrintDetails

())

NcbiCerr

"AnalyzeSeqsViaBioseqs(in_pool_seqs, against_seqs, in_pool_prot, against_prot): " 70

", in_pool_prot= "

<< in_pool_prot

71

", against_prot= "

<< against_prot <<

"\n"

;

83 if

(

PrintDetails

())

NcbiCerr

"AnalyzeSeqsViaBioseqs(in_pool_seqs, against_seqs, in_pool_prot, against_prot): " 104

", against_prot= "

<< against_prot <<

"\n"

;

107 if

((*right)->IsSet())

120 if

( ( against_prot &&

is_prot_entry

((*right)->GetSeq())) ||

188

tblFile = args[

"outTbl"

].AsString();

190

tblFile =

"/dev/null"

;

191

ofstream tblOut(tblFile.c_str(), IOS_BASE::app |

IOS_BASE::out

);

194 if

((*left)->IsSet())

197 NcbiCerr

"AnalyzeSeqs: going down: " 223

CBioseq_set::TSeq_set::iterator right = left;

225 bool

last_right=

false

;

230 if

skip_toprot

(right, seqs)) {last_right=

true

;

break

;}

239

again=

overlaps

((*left)->GetSeq(), (*right)->GetSeq() );

242 if

(last_right)

break

;

244 NcbiCerr

"AnalyzeSeqs: finished lower level seq, overlaps: " 250 if

((*left)->IsSet())

continue

;

254

CBioseq_set::TSeq_set::iterator right = left; ++right;

257 string

common_subject;

258 bool

fit_blast_result =

fit_blast

((*left)->GetSeq(), (*right)->GetSeq(), common_subject);

264 NcbiCerr

"AnalyzeSeqs: after fit_blast:" 272 if

(fit_blast_result)

278 NcbiCerr

"AnalyzeSeqs: finished lower level seq, frameshifts: "

static bool hasProblems(const CBioseq &seq, diagMap &diag, const EProblem type)

static bool PrintDetails(int current_verbosity=m_current_verbosity)

static bool has_blast_hits(const CBioseq &seq)

static void IncreaseVerbosity(void)

bool overlaps_na(const CBioseq::TAnnot &annots)

static int skip_toprot(CTypeIterator< CBioseq > &seq)

static bool is_prot_entry(const CBioseq &seq)

static void DecreaseVerbosity(void)

int AnalyzeSeqsViaBioseqs(bool in_pool_prot, bool against_prot)

int overlaps(const TSimpleSeqs::iterator &seq1, const TSimpleSeqs::iterator &seq2, int &overlap)

static void PopVerbosity(void)

bool overlaps_prot_na(CBioseq &seq, const CBioseq::TAnnot &annots)

bool fit_blast(const CBioseq &left, const CBioseq &right, string &common_subject)

int AnalyzeSeqsViaBioseqs1(CBioseq &left)

static bool skip_to_valid_seq_cand(CBioseq_set::TSeq_set::const_iterator &seq, const CBioseq_set::TSeq_set &seqs)

void append_misc_feature(CBioseq_set::TSeq_set &seqs, const string &name, EProblem problem_type)

static void PushVerbosity(void)

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

main entry point for tests

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TSet & SetSet(void)

Select the variant.

list< CRef< CSeq_entry > > TSeq_set

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsEntrys(void) const

Check if variant Entrys is selected.

string GetStringDescr(const CBioseq &bioseq)

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