Definition in file blast_seqalign.cpp.
#include <ncbi_pch.hpp>
#include "blast_seqalign.hpp"
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/query_data.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objects/general/Object_id.hpp>
#include <serial/iterator.hpp>
#include <objmgr/util/seq_align_util.hpp>
#include <algorithm>
Include dependency graph for blast_seqalign.cpp:
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Defines | |
| #define | SMALLEST_EVALUE 1.0e-180 |
| Threshold below which e-values are saved as 0. | |
| #define | GAP_VALUE -1 |
| Value in the Dense-seg indicating a gap. | |
Functions | |
| USING_SCOPE (objects) | |
| static ENa_strand | s_Frame2Strand (short frame) |
| Converts a frame into the appropriate strand. | |
| static int | s_GetCurrPos (int &pos, int pos2advance) |
| Advances position in a sequence, according to an edit script instruction. | |
| static TSeqPos | s_GetAlignmentStart (int &curr_pos, int num, ENa_strand strand, bool translate, int length, int original_length, short frame) |
| Finds the starting position of a sequence segment in an alignment, given an editing script. | |
| static Int4 | s_GetProteinFrameLength (Int4 nuc_length, Int2 frame) |
| Finds length of a protein frame given a nucleotide length and a frame number. | |
| static void | s_CollectSeqAlignData (const BlastHSP *hsp, const GapEditScript *esp, unsigned int first, unsigned int nsegs, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands, Int4 query_length, Int4 subject_length, bool translate1, bool translate2) |
| Fills vectors of start positions, lengths and strands for all alignment segments. | |
| static void | s_CreateDenseg (CDense_seg &dense_seg, CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands) |
| Creates a Dense-seg object from the starts, lengths and strands vectors and two Seq-ids. | |
| static CSeq_align::C_Segs::TStd | s_CreateStdSegs (CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands, bool translate_master, bool translate_slave) |
| Creates a Std-seg object from the starts, lengths and strands vectors and two Seq-ids for a translated search. | |
| static void | s_CorrectUASequence (BlastHSP *hsp) |
| Checks if any decline-to-align segments immediately follow an insertion or deletion, and swaps any such segments so indels are always to the right of the decline-to-align segments. | |
| static CRef< CSeq_align > | s_CreateSeqAlign (CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > starts, vector< TSeqPos > lengths, vector< ENa_strand > strands, bool translate_master, bool translate_slave) |
| Creates a Seq-align for a single HSP from precalculated vectors of start positions, lengths and strands of segments, sequence identifiers and other information. | |
| static CRef< CSeq_align > | s_BlastHSP2SeqAlign (EBlastProgramType program, BlastHSP *hsp, CRef< CSeq_id > id1, CRef< CSeq_id > id2, Int4 query_length, Int4 subject_length) |
| Converts a traceback editing block to a Seq-align, provided the 2 sequence identifiers. | |
| static CRef< CSeq_align > | s_OOFBlastHSP2SeqAlign (EBlastProgramType program, BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length) |
| This function is used for out-of-frame traceback conversion Converts an OOF editing script chain to a Seq-align of type Std-seg. | |
| static CRef< CScore > | s_MakeScore (const string &ident_string, double d=0.0, int i=0) |
| Creates and initializes CScore with a given name, and with integer or double value. | |
| static size_t | s_CalculateScoreVectorSize (const BlastHSP *hsp, const vector< int > &gi_list) |
| Computes the exact size of a CSeq_align::TScore for a given HSP. | |
| static void | s_BuildScoreList (const BlastHSP *hsp, CSeq_align::TScore &scores, const vector< int > &gi_list) |
| Creates a list of score objects for a Seq-align, given an HSP structure. | |
| static void | s_AddScoresToSeqAlign (CRef< CSeq_align > &seqalign, const BlastHSP *hsp, const vector< int > &gi_list) |
| Given an HSP structure, creates a list of scores and inserts them into a Seq-align. | |
| CRef< CDense_diag > | x_UngappedHSPToDenseDiag (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list) |
| Creates a Dense-diag object from HSP information and sequence identifiers for a non-translated ungapped search. | |
| CRef< CStd_seg > | x_UngappedHSPToStdSeg (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list) |
| Creates a Std-seg object from HSP information and sequence identifiers for a translated ungapped search. | |
| void | BLASTUngappedHspListToSeqAlign (EBlastProgramType program, BlastHSPList *hsp_list, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list, vector< CRef< CSeq_align > > &sa_vector) |
| Creates a Seq-align from an HSP list for an ungapped search. | |
| void | BLASTHspListToSeqAlign (EBlastProgramType program, BlastHSPList *hsp_list, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, bool is_ooframe, const vector< int > &gi_list, vector< CRef< CSeq_align > > &sa_vector) |
| This is called for each query and each subject in a BLAST search. | |
| static CRef< CSeq_align_set > | s_CreateEmptySeq_align_set () |
| void | RemapToQueryLoc (CRef< CSeq_align > sar, const CSeq_loc &query) |
| Remaps Seq-align offsets relative to the query Seq-loc. | |
| static void | s_RemapToSubjectLoc (CRef< CSeq_align > &subj_aligns, const CSeq_loc &subj_loc) |
| Remap subject alignment if its location specified the reverse strand or a starting location other than the beginning of the sequence. | |
| CRef< CSeq_align_set > | BlastHitList2SeqAlign_OMF (const BlastHitList *hit_list, EBlastProgramType prog, const CSeq_loc &query_loc, TSeqPos query_length, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, TSeqLocInfoVector &subj_masks) |
| TSeqAlignVector | PhiBlastResults2SeqAlign_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query, const IBlastSeqInfoSrc *seqinfo_src, const SPHIQueryInfo *pattern_info, vector< TSeqLocInfoVector > &subj_masks) |
| static void | s_AdjustNegativeSubjFrameInBlastn (ENa_strand subj_strand, EBlastProgramType program, BlastHSPList *hsp_list) |
| This function changes the subject frame for HSPs if the program is blastn and the subject was specified with a negative strand. | |
| static TSeqAlignVector | s_BLAST_OneSubjectResults2CSeqAlign (const BlastHSPResults *results, ILocalQueryData &query_data, const IBlastSeqInfoSrc &seqinfo_src, EBlastProgramType prog, Uint4 subj_idx, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks) |
| Extracts results from the BlastHSPResults structure for only one subject sequence, identified by its index, and converts them into a vector of CSeq_align_set objects. | |
| static TSeqAlignVector | s_TransposeSeqAlignVector (const TSeqAlignVector &alnvec, const size_t num_queries, const size_t num_subjects) |
| Transpose the (linearly organized) seqalign set matrix from (q1 s1 q2 s1 . | |
| static TSeqAlignVector | s_BlastResults2SeqAlignSequenceCmp_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query_data, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks) |
| static TSeqAlignVector | s_BlastResults2SeqAlignDatabaseSearch_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks) |
| TSeqAlignVector | LocalBlastResults2SeqAlign (BlastHSPResults *hsp_results, ILocalQueryData &local_data, const IBlastSeqInfoSrc &seqinfo_src, EBlastProgramType program, bool gapped, bool oof_mode, vector< TSeqLocInfoVector > &subj_masks, EResultType result_type=eDatabaseSearch) |
| Convert traceback output into Seq-align format. | |
Variables | |
| static const TSeqPos | kBlastAlignmentDim = 2 |
| BLAST alignments have always 2 dimensions (i.e. | |
1.4.6
Modified on Mon Dec 07 16:21:37 2009 by modify_doxy.py rev. 173732