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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/prosplign_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/align/prosplign/prosplign.hpp Source File

1 #ifndef ALGO_ALIGN_PROSPLIGN__HPP 2 #define ALGO_ALIGN_PROSPLIGN__HPP 63 const string

& GetScoreMatrix()

const

;

66 bool

GetAltStarts()

const

;

88 int

GetMinIntronLen()

const

;

94 int

GetGapOpeningCost()

const

;

98 int

GetGapExtensionCost()

const

;

101 int

GetFrameshiftOpeningCost()

const

;

105 int

GetGTIntronCost()

const

;

108 int

GetGCIntronCost()

const

;

111 int

GetATIntronCost()

const

;

117 int

GetNonConsensusIntronCost()

const

;

122 int

GetInvertedIntronExtensionCost()

const

;

125 static const int

default_min_intron_len = 30;

127 static const int

default_gap_opening = 10;

128 static const int

default_gap_extension = 1;

129 static const int

default_frameshift_opening = 30;

131 static const int

default_intron_GT = 15;

132 static const int

default_intron_GC = 20;

133 static const int

default_intron_AT = 25;

134 static const int

default_intron_non_consensus = 34;

135 static const int

default_inverted_intron_extension = 1000;

170 bool

IsPassThrough()

const

;

175 bool

GetCutFlanksWithPositDrop()

const

;

177 int

GetCutFlanksWithPositDropoff()

const

;

180 int

GetCutFlanksWithPositWindow()

const

;

183 int

GetCutFlanksWithPositMaxLen()

const

;

186 int

GetCutFlanksWithPositGapRatio()

const

;

191 bool

GetCutFlankPartialCodons()

const

;

196 bool

GetFillHoles()

const

;

203 int

GetMinHoleLen()

const

;

208 bool

GetCutNs()

const

;

212 int

GetFlankPositives()

const

;

215 int

GetTotalPositives()

const

;

219 int

GetMaxBadLen()

const

;

221 int

GetMinPositives()

const

;

225 int

GetMinExonId()

const

;

228 int

GetMinExonPos()

const

;

232 int

GetMinFlankingExonLen()

const

;

235 int

GetMinGoodLen()

const

;

239 int

GetStartBonus()

const

;

242 int

GetStopBonus()

const

;

245 static const bool

default_cut_flanks_with_posit_drop =

true

;

246 static const int

default_cut_flanks_with_posit_dropoff = 35;

247 static const int

default_cut_flanks_with_posit_window = 90;

248 static const int

default_cut_flanks_with_posit_max_len = 30;

249 static const int

default_cut_flanks_with_posit_gap_ratio = 2;

251 static const bool

default_cut_flank_partial_codons =

true

;

252 static const bool

default_fill_holes =

false

;

253 static const int

default_min_hole_len = 200;

254 static const bool

default_cut_ns =

false

;

256 static const int

default_flank_positives = 55;

257 static const int

default_total_positives = 70;

259 static const int

default_max_bad_len = 45;

260 static const int

default_min_positives = 15;

262 static const int

default_min_exon_id = 30;

263 static const int

default_min_exon_pos = 55;

265 static const int

default_min_flanking_exon_len = 15;

266 static const int

default_min_good_len = 59;

268 static const int

default_start_bonus = 8;

269 static const int

default_stop_bonus = 8;

307 void

SetTranslationTable(

int

gcode);

314 void

Interrupt(

void

);

327 const

objects::CSeq_id& protein,

328 const

objects::CSeq_loc& genomic,

332

align_ref = FindGlobalAlignment(scope, protein, genomic);

342

FindGlobalAlignment(objects::CScope& scope,

343 const

objects::CSeq_id& protein,

344 const

objects::CSeq_loc& genomic);

350 const

objects::CSeq_align& seq_align,

355

objects::CSeq_align& seq_align,

362 void

AssignGeneticCode(objects::CScope& scope,

const

objects::CSeq_id& gid,

int

gcode);

367 const

vector<pair<int, int> >& GetExons()

const

;

368

vector<pair<int, int> >& SetExons();

369 void

GetFlanks(

bool

& lgap,

bool

& rgap)

const

;

370 void

SetFlanks(

bool

lgap,

bool

rgap);

373 class

CImplementation;

393 static void

Output(

const

objects::CSeq_align& seqalign, objects::CScope& scope, ostream&

out

int

width,

const string

& matrix_name =

"BLOSUM62"

);

void RefineAlignment(objects::CScope &scope, objects::CSeq_align &seq_align, const list< CNPiece > &good_parts)

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)

Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...

Scoring parameters object.

static void SetupArgDescriptions(CArgDescriptions *argdescr)

static const bool default_allow_alt_starts

static const char * default_score_matrix_name

Output filtering parameters.

bool cut_flanks_with_posit_drop

???

int cut_flanks_with_posit_max_len

int cut_flanks_with_posit_window

int cut_flanks_with_posit_gap_ratio

bool cut_flank_partial_codons

int min_flanking_exon_len

@ ePassThrough

all zeroes - no filtering

@ eWithHoles

default filtering parameters

int cut_flanks_with_posit_dropoff

int inverted_intron_extension

Text representation of ProSplign alignment.

spliced protein to genomic alignment

CProSplign & operator=(const CProSplign &)

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

unique_ptr< CImplementation > m_implementation

CProSplign(const CProSplign &)

forbidden

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

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

main entry point for tests

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XALGOALIGN_EXPORT

Defines command line argument related classes.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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