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NCBI C++ ToolKit: src/objtools/alnmgr/alnvec.cpp Source File

m_set_GapChar(

),

m_set_EndChar(

),

m_set_GapChar(

),

m_set_EndChar(

),

errstr =

(

)

+

seq_vec = iter->second;

(

=0;

<chunk_vec->size();

++) {

(chunk->GetType() &

) {

seq_vec.

(chunk->GetRange().GetFrom(),

chunk->GetRange().GetTo() + 1,

seq_vec.

(seq_vec_size - chunk->GetRange().GetTo() - 1,

seq_vec_size - chunk->GetRange().GetFrom(),

= chunk->GetAlnRange().GetLength();

* ch_buff =

[

+1];

memset(ch_buff, fill_ch,

);

scrn_width,

scrn_lft_seq_pos = -1,

scrn_rgt_seq_pos = -1,

pos, nscrns,

;

record_inserts = insert_starts && insert_lens;

record_coords = scrn_width && scrn_lefts && scrn_rights;

(seg = 0, pos =

, aln_pos = 0, anchor_pos =

;

= seg_len * width;

(anchored &&

[anchor_pos] < 0) {

(record_inserts) {

prev_start -

)) {

insert_lens->pop_back();

insert_lens->push_back(ttl_len);

insert_starts->pop_back();

insert_starts->push_back(start);

prev_aln_pos = aln_pos / width;

insert_starts->push_back(start);

insert_aln_starts->push_back(prev_aln_pos);

insert_lens->push_back(

);

stop = start +

- 1;

(buf_len < seg_len) {

buf_len = seg_len - buf_len;

(seg < left_seg || seg > right_seg) {

(

= 0;

< buf_len; ++

) {

(scrn_lft_seq_pos < 0) {

scrn_lft_seq_pos =

? start : stop;

(scrn_rgt_seq_pos < 0) {

scrn_rgt_seq_pos = scrn_lft_seq_pos;

nscrns = (aln_pos - scrn_pos) / scrn_width;

(

= 0;

< nscrns;

++) {

scrn_lefts->push_back(scrn_lft_seq_pos);

scrn_rights->push_back(scrn_rgt_seq_pos);

scrn_lft_seq_pos =

? start : stop;

scrn_pos += scrn_width;

scrn_lft_seq_pos =

? start : stop;

nscrns = (aln_pos +

- scrn_pos) / scrn_width;

(

= 0;

< nscrns;

++) {

scrn_width - (curr_pos - scrn_pos) :

curr_pos - scrn_pos - scrn_width);

scrn_lefts->push_back(scrn_lft_seq_pos);

scrn_lft_seq_pos < start :

scrn_lft_seq_pos > stop) {

scrn_lft_seq_pos = (

? start : stop) +

scrn_rgt_seq_pos = scrn_lft_seq_pos +

scrn_rgt_seq_pos = scrn_lft_seq_pos + (

? -1 : 1)

scrn_lft_seq_pos +=

;

(seg == left_seg &&

scrn_lft_seq_pos == scrn_rgt_seq_pos) {

scrn_rights->push_back(scrn_rgt_seq_pos);

curr_pos = scrn_pos += scrn_width;

(aln_pos +

<= scrn_pos) {

scrn_lft_seq_pos = -1;

scrn_rgt_seq_pos =

? stop : start;

(seg < left_seg || seg > right_seg) {

(

= 0;

< seg_len; ++

) {

pos_diff = aln_pos - scrn_pos;

nscrns = pos_diff / scrn_width;

(pos_diff % scrn_width) {

(

= 0;

< nscrns;

++) {

scrn_lefts->push_back(scrn_lft_seq_pos);

scrn_rights->push_back(scrn_rgt_seq_pos);

scrn_lft_seq_pos = scrn_rgt_seq_pos;

scrn_pos += scrn_width;

vector<string>* consens)

consensus_seq.

();

(consens ==

) {

(

= 0;

< consens->size(); ++

) {

(j = 0; j < (size_t)

; ++j) {

((*consens)[

].length() != 0) {

new_ds->

().push_back(total_bases);

+= (*consens)[

];

(

= 0;

<

.size(); ++

) {

->Assign(consensus_id);

consensus_seq.

().push_back(

);

new_ds->

().push_back(

);

desc.

().push_back(d);

d->

(

);

consensus_row =

(new_ds->

().size()) - 1;

rows = segs.size();

(

= 0;

< rows; ++

) {

& s = segs[

];

=

[(rows+1)*(cols+1)];

* src = s.c_str();

* dst =

+(

-gap_rows);

((*dst = *src++)) {

(

col = 0; col < cols; ++col) {

* col_buf =

+ col*(rows+1);

*(col_buf+(rows-gap_rows)) = 0;

segs.push_back(

(col_buf));

fill_n(base_count, numBases, 0);

*

= col.c_str();

((c = *

++)) {

fill_n(base_count, numBases, 0);

*

= col.c_str();

((c = *

++)) {

(0<=pos && pos < numBases)

numBases = isNucleotide ? 4 : 26;

(

j = 0; j < (size_t)

; ++j) {

( gap_count > gap_seg_thresh )

consens[j].resize(

[j]);

(

= 0;

<

[j]; ++

) {

(

k = 0; k < numBases; ++k) {

(rev_map.count(rev_map.begin()->first) == 1 &&

rev_map.begin()->first >= base_thresh) {

consens[j][

] = isNucleotide ?

(rev_map.begin()->second) :

(rev_map.begin()->second+

);

c = 0x00;

TRevMap::iterator curr = rev_map.begin();

TRevMap::iterator

= rev_map.begin();

curr != rev_map.end() &&

(freq < base_thresh ||

->first == curr->first);

cur_char = curr->second+

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

consens[j][

] = isNucleotide ?

:

;

consens[j][

] = isNucleotide ?

(c) : c;

segment_row_index = segment*

;

(

= 0;

< (size_t)

; ++

, ++segment_row_index) {

& s = segs[

];

& consensus_id)

*bioseq, consensus_id);

s1_is_prot,

s2_is_prot,

gen_code1,

gen_code2)

(s1_is_prot == s2_is_prot && s1.length() != s2.length()) {

);

}

(s1.length() * (s1_is_prot ? 1 : 3) !=

s2.length() * (s2_is_prot ? 1 : 3)) {

);

* res1 = (

*) s1.c_str();

* res2 = (

*) s2.c_str();

* end1 = res1 + s1.length();

* end2 = res2 + s2.length();

s_FullScoreMatrixInitialized =

;

(s1_is_prot && s2_is_prot) {

( !s_FullScoreMatrixInitialized ) {

s_FullScoreMatrixInitialized =

;

( ; res1 != end1; res1++, res2++) {

}

( !s1_is_prot && !s2_is_prot ) {

( ; res1 != end1; res1++, res2++) {

(*res1 == *res2) {

( ; res1 != end1; res1++, res2++) {

( ; res2 != end2; res1++, res2++) {

);

na_size = na.size();

aa.resize(na_size / 3);

(

na_i = 0; na_i < na_size; ) {

(

= 0;

< 3;

++) {

index1 = row1, index2 = row2;

(start1 >=0 && start2 >= 0) {

gaps_in_count)

na_buff, aa_buff;

(residue_count) {

(gaps_in_count && residue_count) {

residue_cnt.resize(16, 0);

= 0, total = 0;

(*i_res >

) {

100 *

/ total;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

static SNCBIFullScoreMatrix s_FullScoreMatrix

bool IsSetAnchor(void) const

list< TSeqPos > TSeqPosList

int GetWidth(TNumrow row) const

const TNumseg & x_GetSeqLeftSeg(TNumrow row) const

const CDense_seg::TStarts & m_Starts

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

bool IsPositiveStrand(TNumrow row) const

const CDense_seg::TIds & m_Ids

TNumseg GetSeg(TSeqPos aln_pos) const

TDim GetNumRows(void) const

const CDense_seg::TStrands & m_Strands

CConstRef< CDense_seg > m_DS

const TNumseg & x_GetSeqRightSeg(TNumrow row) const

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

unsigned int TSegTypeFlags

TSeqPos GetAlnStart(void) const

TSeqPos GetLen(TNumseg seg, int offset=0) const

CDense_seg::TNumseg TNumseg

TSeqPos GetAlnStop(void) const

const CDense_seg::TLens & m_Lens

static void CollectNucleotideFrequences(const string &col, int base_count[], int numBases)

CAlnVec(const CDense_seg &ds, CScope &scope)

const CBioseq_Handle & GetBioseqHandle(TNumrow row) const

TResidue GetGapChar(TNumrow row) const

string & GetSeqString(string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const

TResidue GetEndChar() const

static void TranslateNAToAA(const string &na, string &aa, int gen_code=kDefaultGenCode)

int GetGenCode(TNumrow row) const

string & GetColumnVector(string &buffer, TSeqPos aln_pos, TResidueCount *residue_count=0, bool gaps_in_count=false) const

string & GetWholeAlnSeqString(TNumrow row, string &buffer, TSeqPosList *insert_aln_starts=0, TSeqPosList *insert_starts=0, TSeqPosList *insert_lens=0, unsigned int scrn_width=0, TSeqPosList *scrn_lefts=0, TSeqPosList *scrn_rights=0) const

CSeqVector & x_GetSeqVector(TNumrow row) const

CScope & GetScope(void) const

static void CollectProteinFrequences(const string &col, int base_count[], int numBases)

static unsigned char ToIupac(unsigned char c)

CRef< CDense_seg > CreateConsensus(int &consensus_row) const

string & GetAlnSeqString(string &buffer, TNumrow row, const CAlnMap::TSignedRange &aln_rng) const

int CalculateScore(TNumrow row1, TNumrow row2) const

void RetrieveSegmentSequences(size_t segment, vector< string > &segs) const

TBioseqHandleCache m_BioseqHandlesCache

vector< int > TResidueCount

static unsigned char FromIupac(unsigned char c)

TSeqVectorCache m_SeqVectorCache

int CalculatePercentIdentity(TSeqPos aln_pos) const

static void TransposeSequences(vector< string > &segs)

static const CTrans_table & GetTransTable(int id)

@Seq_descr.hpp User-defined methods of the data storage class.

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * column

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string AsFastaString(void) const

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

void SetCoding(TCoding coding)

void SetIupacCoding(void)

Set coding to either Iupacaa or Iupacna depending on molecule type.

bool IsNucleotide(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetDim(TDim value)

Assign a value to Dim data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

TIds & SetIds(void)

Assign a value to Ids data member.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

TIupacna & SetIupacna(void)

Select the variant.

TMol GetMol(void) const

Get the Mol member data.

TComment & SetComment(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

virtual void Reset(void)

Reset the whole object.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

Tdata & Set(void)

Assign a value to data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

TIupacaa & SetIupacaa(void)

Select the variant.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_raw

continuous sequence

@ e_not_set

No variant selected.

@ eMol_na

just a nucleic acid

unsigned int

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

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

Int4 delta(size_t dimension_, const Int4 *score_)

const SNCBIPackedScoreMatrix NCBISM_Blosum62

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

#define row(bind, expected)

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