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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fit__blast_8cpp_source.html below:

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

40 string

& common_subject

75 getFromTo

(left_genomic_int, from1, to1, left_strand);

76 getFromTo

(right_genomic_int, from2, to2, right_strand);

78 int

left_frame = (from1-1)%3+1;

79 int

right_frame = (from2-1)%3+1;

82 if

(left_strand != right_strand)

94 int

space = ((

int

)from2-(

int

)to1)/3+1;

98 int

num=0, numFit=0, numGI=0;

99 int

numLeft=0, numRight=0;

100

vector<perfectHitStr> left_perfect;

101

vector<perfectHitStr> right_perfect;

106 int

n_frameshift_pairs=0;

107

list<problemStr> problemsl;

108

list<problemStr> problemsr;

111 string

any_common_subject=

""

;

115 if

(!(*left_annot)->GetData().IsAlign())

continue

;

118

vector<long> left_gis =

getGIs

(left_annot);

125 if

(!(*right_annot)->GetData().IsAlign())

continue

;

128

vector<long> right_gis =

getGIs

(right_annot);

131 if

giMatch

(left_gis, right_gis))

142

report->

s_id

= left_gis[0];

148 int

frame_to =frame_from;

159 if

( (!reverse &&

fit_blast

(left, right, left_annot, right_annot, left_qLen, right_qLen, space, report)) ||

160

( reverse &&

fit_blast

(right, left, right_annot, left_annot, right_qLen, left_qLen, space, report))

165 if

(numFit==1) any_common_subject = this_subject;

166 if

(common_subject.size()==0 && this_subject.find(

"hypothetical"

)==string::npos)

169

common_subject = this_subject;

170 if

(

PrintDetails

())

NcbiCerr

"zero common_subject changed to non-hypothetical this_subject "

<< this_subject

175 char

bufferchar[20480]; memset(bufferchar, 0, 20480);

176

strstream

buffer

(bufferchar, 20480);

179 if

(common_subject.size())

181

misc_feat <<

"potential frameshift: common BLAST hit: " 182

<< common_subject <<

'\0'

;

197

problemsl.push_back(problem);

201

problemsr.push_back(problem);

203

n_frameshift_pairs++;

211

num=numLeft*numRight;

212 if

(common_subject.size()==0) common_subject = any_common_subject;

218 if

(qname.find(

"hypothetical"

) != string::npos || qrname.find(

"hypothetical"

) != string::npos)

221

"one of those is hypo: FRAMESHIFT"

NcbiEndl

;

230

"numFit < 2: NOT A FRAMESHIFT"

NcbiEndl

;

236 if

(left_perfect.size() || right_perfect.size())

239

"there are exhonerating hits: NOT A FRAMESHIFT"

NcbiEndl

;

246

"there are no exhonerating hits: FRAMESHIFT"

NcbiEndl

;

255

"numFit = 0: NOT A FRAMESHIFT"

NcbiEndl

;

265 char

bufferchar[2048]; memset(bufferchar, 0, 2048);

266

strstream

buffer

(bufferchar, 2048);

267 buffer

"Left sequence has "

<< left_perfect.size() <<

" perfect hits."

NcbiEndl

;

268 ITERATE

(vector<perfectHitStr>, hit, left_perfect)

272 buffer

"Right sequence has "

<< right_perfect.size() <<

" perfect hits."

NcbiEndl

;

273 ITERATE

(vector<perfectHitStr>, hit, right_perfect)

277 buffer

"In total, "

<< numFit <<

" pairs of hits (out of "

<< num <<

") match for these two sequences."

NcbiEndl

;

294

CBioseq::TAnnot::const_iterator& left_annot,

295

CBioseq::TAnnot::const_iterator& right_annot,

296 int

left_qLen,

int

right_qLen,

311 int

left_qFrom, left_qTo, right_qFrom, right_qTo;

312 int

left_sFrom, left_sTo, right_sFrom, right_sTo;

313 getBounds

(left_annot, &left_qFrom, &left_qTo, &left_sFrom, &left_sTo);

314 getBounds

(right_annot, &right_qFrom, &right_qTo, &right_sFrom, &right_sTo);

320

report->

space

= space;

321

report->

s_name

"cannot get subject name"

;

366 result

= result_left > 0 && result_right > 0;

static bool PrintDetails(int current_verbosity=m_current_verbosity)

static string GetProtName(const CBioseq &seq)

static bool giMatch(const vector< long > &left, const vector< long > &right)

static int getQueryLen(const CBioseq &seq)

static vector< long > getGIs(CBioseq::TAnnot::const_iterator &annot)

static bool has_blast_hits(const CBioseq &seq)

static void IncreaseVerbosity(void)

static int collectPerfectHits(vector< perfectHitStr > &perfect, const CBioseq &seq)

static string getAnnotComment(CBioseq::TAnnot::const_iterator &annot)

static string getAnnotName(CBioseq::TAnnot::const_iterator &annot)

static bool hasGenomicLocation(const CBioseq &seq)

static void DecreaseVerbosity(void)

static void getBounds(CBioseq::TAnnot::const_iterator &annot, int *qFrom, int *qTo, int *sFrom, int *sTo)

static void printPerfectHit(const perfectHitStr &hit, ostream &out=NcbiCout)

static void PopVerbosity(void)

static const CSeq_loc & getGenomicLocation(const CBioseq &seq)

static void printReport(distanceReportStr *report, ostream &out=NcbiCout)

static int getLenScore(CBioseq::TAnnot::const_iterator &annot)

static void getFromTo(const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)

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

static void PushVerbosity(void)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

ENa_strand

strand of nucleic acid

const TInst & GetInst(void) const

Get the Inst member data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TMol GetMol(void) const

Get the Mol member data.

list< CRef< CSeq_annot > > TAnnot

unsigned int

A callback function used to compare two keys in a database.

int addProblems(list< problemStr > &dest, const list< problemStr > &src)

string GetStringDescr(const CBioseq &bioseq)

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