Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/primercheck_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/primer/primercheck.hpp Source File

CPrimercheckTest;

pair<vector<SHspInfo*>, vector<SHspInfo*> >

;

allowed_total_mismatch = 1,

allowed_3end_mismatch = 1,

m_TemplateRange = range;

m_TargetSizeMax =

;

allowed_3end_mismatch) {

m_AllowedTotalMismatch = allowed_total_mismatch;

m_Allowed3EndMismatch = allowed_3end_mismatch;

m_MaxMismatch = max_mismatch;

m_AllowedSeqidIndex = allowed_seqid_index;

m_AllowedSeqloc = allowed_seq;

m_Allowed_Splice_Variants = allowed_splice_variants;

m_NumNonSpecificTarget =

;

m_MaxTargetPerSequence =

;

m_MismatchRegionLength3End = length;

CheckSpecificity(

vector<SPrimerInfo>& primer_info_list,

from = 0,

to = -1);

x_AnalyzePrimerSpecificity();

x_AnalyzeTwoPrimers(

& sorted_hsp,

x_AnalyzeOnePrimer(

vector<SHspInfo*>& plus_strand_hsp_list,

vector<SHspInfo*>& minus_strand_hsp_list,

HspOverlappingWithLeftPrimer_size,

HspOverlappingWithRightPrimer_size,

HspOverlappingWithLeftPrimerMinusStrand_size,

HspOverlappingWithRightPrimerMinusStrand_size,

x_IsPcrLengthInRange(

& left_primer_hit_align,

primers_on_different_strand,

x_SavePrimerInfo(

& left_align,

is_self_forward_primer,

is_self_reverse_primer);

x_AnalyzeLeftAndRightPrimer(

vector<SHspInfo*>& hsp_list,

HspOverlappingWithLeftPrimer_size,

HspOverlappingWithRightPrimer_size,

get_master_range,

x_FindOverlappingHSP(

* left_window_index_list,

& left_window_index_list_size,

& right_window_index_list_size,

vector<SHspInfo*>& hsp_list);

x_SortPrimerHit(vector<vector<SPrimerHitInfo> >& primer_hit_list_list);

x_FindMatchInfoForAlignment(

& primer_denseg,

& max_num_continuous_match,

& max_num_continuous_match,

& nw_align_modified);

class ::CPrimercheckTest;

TSeqPos m_ActualProductLen

the actual length of the pcr product on the input template

const SPrimerInfo * m_PrimerInfo

const vector< vector< SPrimerHitInfo > > & GetTranscriptVariantTargetList() const

return the hits that represent the transcript variant from the same gene as the input pcr template.

const COligoSpecificityTemplate * m_Hits

the information about the blast results

SHspIndexInfo * m_HspOverlappingWithLeftPrimer

CRef< CScope > m_Scope

scope to fetch sequence

SHspIndexInfo * m_HspOverlappingWithLeftPrimerMinusStrand

pair< CRef< CSeq_align >, CRef< CSeq_align > > TAlignmentPair

vector< vector< SPrimerHitInfo > > m_SelfHit

the hit represent the input template

vector< vector< SPrimerHitInfo > > m_VariantHit

the hits represent the transcript variants from the same gene as the input template

CRef< CScope > m_FeatureScope

void x_GetCachedAlnRange(CRange< TSeqPos > &master_range, CRange< TSeqPos > &hit_range, bool get_master_range, bool get_hit_range, const CSeq_align &input_hit)

const vector< vector< SPrimerHitInfo > > & GetNonSpecificTargetList() const

return the non-specific hits that the primer pairs can amplify

SHspIndexInfo * m_HspOverlappingWithRightPrimerMinusStrand

TSeqPos m_SpecifiedProductLen

the requested pcr length for non-specific template

vector< map< SSlaveRange, CRange< TSeqPos >, slave_range_sort_order > > m_SlaveRangeCache

vector< vector< SPrimerHitInfo > > m_PrimerHit

the non-specific hit for the primer pair

vector< int > m_NumTargetFromSameSequence

max number of targets allowed from a single subject sequence for a primer.

vector< const SPrimerInfo * > m_PrimerInfoList

the information about primer to be checked

CRef< CObjectManager > m_FeatureOM

const vector< vector< SPrimerHitInfo > > & GetAllowedTargetList() const

return the hits the primer pair can amplify but users want to ignore for specificity

map< SAlnCache, SPrimerMatch, sort_order > m_Cache

cache coordinate-alignment mapping

const vector< vector< SPrimerHitInfo > > & GetSelfTargetList() const

retrun the hit whose seqid is the same as the template hit itself.

SHspIndexInfo * m_HspOverlappingWithRightPrimer

vector< vector< SPrimerHitInfo > > m_AllowedHit

the hit that user choose to ingnore for specificity

int m_NumNonSpecificTarget

the number non-specific targets to return

void SetAllowedSeq(const list< CRef< CSeq_loc > > *allowed_seq)

TSeqPos m_Allowed3EndMismatch

3' end mismatches

CRange< TSeqPos > m_TemplateRange

range on the input template

CConstRef< CSeq_id > m_Id

seqid

void SetAllowedMismatch(TSeqPos allowed_total_mismatch, TSeqPos allowed_3end_mismatch)

Set mismatch threshhold below which a primer hit pair representing a PCR product will be reported.

TSeqPos m_MismatchRegionLength3End

the length or region at the 3' end for checking mismatches

TSeqPos m_MaxMismatch

total max allowed mismatch

vector< TSeqPos > m_AllowedSeqidIndex

user specified hits that can be disregarded for specificity checking

CSeq_id::EAccessionInfo m_TemplateType

void SetMaxMismatchDetection(TSeqPos max_mismatch)

const CBioseq_Handle & m_TemplateHandle

bioseq handle for input bioseq

vector< TSortedHsp > m_SortHit

the processed sorted hit list corresponding to the input seqalign

void SetAllowedSeqid(const vector< TSeqPos > &allowed_seqid_index)

Allowed seqid will not be counted as non-specific hits.

const list< CRef< CSeq_id > > * m_Allowed_Splice_Variants

TSeqPos m_AllowedTotalMismatch

total mismatches allowed by user

void SetAllowedSpliceVariants(const list< CRef< CSeq_id > > *allowed_splice_variants)

TSeqPos m_TargetSizeMax

the requested target max length

int m_WordSize

minimal continuous match required

int m_MaxTargetPerSequence

void SetTemplateRange(CRange< TSeqPos > range)

Set start and end position of the input PCR template.

const list< CRef< CSeq_loc > > * m_AllowedSeqloc

void SetNumNonSpecificTargets(int number)

The maximal number of non-specific targets to return.

void SetTargetSize(TSeqPos max)

Set the allowed pcr product size range.

void SetMaxTargetPerSequence(int number)

internal default 100

void SetMismatchRegionLength3End(TSeqPos length)

the length of region at the 3' end of primer during which the mismatched are counted.

vector< CIntervalTree * > m_RangeTreeListMinusStrand

vector< CIntervalTree * > m_RangeTreeListPlusStrand

unsigned int TSeqPos

Type for sequence locations and lengths.

EAccessionInfo

For IdentifyAccession (below)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XPRIMER_EXPORT

ENa_strand

strand of nucleic acid

pair< vector< SHspInfo * >, vector< SHspInfo * > > TSortedHsp

key for coordinate-alignment cache

primer hit to the blast dababase

TSeqPos left_3end_mismatch

TSeqPos left_total_mismatch

TSeqPos right_total_mismatch

TSeqPos right_3end_mismatch

the input primer pair information only the left and right range information is needed by this API

int left_primer_genomic_exon_end

int right_primer_genomic_exon_end

int right_primer_genomic_exon_start

double internal_probe_gc_percent

double product_tm_oligo_tm_diff

double right_self_complementarity_any

double pair_complementarity_any

double left_self_complementarity_any

int left_primer_splice_site_pos

int right_primer_splice_site_pos

int left_primer_genomic_exon_start

string internal_probe_seq

CRange< TSeqPos > internal_probe

double pair_complementarity_3end

double left_self_complementarity_3end

double right_self_complementarity_3end

value for coordinate-alignment cache

TSeqPos num_3end_mismatch

total mismatchs

CRef< CSeq_align > aln

3' end gaps

TSeqPos num_3end_gap

total gaps

TSeqPos num_total_mismatch

TSeqPos num_total_gap

3' end mismatches

const CSeq_align * align_index

bool operator()(const SSlaveRange s1, const SSlaveRange s2) const

strict weak ordering functor

bool operator()(const SAlnCache s1, const SAlnCache s2) const

CRange< TSeqPos > master_range

CRange< TSeqPos > slave_range

CConstRef< CSeq_align > hsp

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4