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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSeqAnnotFromFasta.cpp Source File

= sequence.length();

nGaps = 0;

vector<unsigned int>::const_iterator posBeg = positions.begin(), posEnd = positions.end();

numNonAlpha.

();

(

= 0;

<

; ++

) {

(find(posBeg, posEnd,

) != posEnd) {

numNonAlpha[

] = nGaps;

aa =

((

) sequence[

]);

numNonAlpha[

] = nGaps;

builtIt =

;

(dummyCD.

().

().size() == 0) {

global->SetAccession(

);

global->SetVersion(0);

dummyCD.

().Set().push_back(cdId);

dummyCD.

(

);

builtIt =

;

, j,

, maxLen;

masterSequence, sequence;

vector<unsigned int> residueCount;

nBlocks;

vector<unsigned int> blockStarts;

vector<unsigned int> blockLengths;

maxLen = (maxLenIndex < nSeq) ?

[maxLenIndex].length() : 0;

residueCount.resize(maxLen);

(

= 0;

< nSeq; ++

) {

= sequence.length();

(j = 0; j <

; ++j) {

uc =

((

) sequence[j]);

nBlocks =

(nSeq, residueCount, forcedBreaks, blockStarts, blockLengths);

(nBlocks == 0 || nBlocks != blockLengths.size())

;

(

= 0;

< nSeq; ++

) {

aligns.push_back(sa);

(

<<

);

aligns.push_back(sa);

(

<<

);

(aligns.size() == nSeq - 1 || (nSeq == 1 && aligns.size() == nSeq)) {

(

);

(

);

builtIt =

;

, j,

, maxLen, masterLen;

sequence, masterSequence;

vector<unsigned int> residueCount, masterResidueCount;

nBlocks;

vector<unsigned int> blockStarts;

vector<unsigned int> blockLengths;

masterLen = masterSequence.length();

masterResidueCount.assign(masterLen, 0);

(j = 0; j < masterLen; ++j) {

uc =

((

) masterSequence[j]);

++masterResidueCount[j];

(

= 0;

< nSeq; ++

) {

blockLengths.clear();

nBlocks =

(1, masterResidueCount, forcedBreaks, blockStarts, blockLengths);

(nBlocks == 0)

;

aligns.push_back(sa);

(

<<

);

residueCount.assign(maxLen, 0);

=

((

)sequence.length(), masterLen);

(j = 0; j <

; ++j) {

uc =

((

) sequence[j]);

(

(uc) && masterResidueCount[j] > 0) {

blockLengths.clear();

(nBlocks == 0)

;

aligns.push_back(pairwiseSA);

(aligns.size() == nSeq - 1 || (nSeq == 1 && aligns.size() == nSeq)) {

(

);

(

);

masterIndex = 0;

, j, maxLen, nSeq, nStructs;

nAlignedMax, nGapsMin, nGaps;

firstCommon, lastCommon;

vector<unsigned int> isConsidered;

vector<unsigned int> nGapsBySeq, nAlignedBySeq, nAlignedByCol, lengths;

vector<string> tmpSeqs;

(

= 0;

< nSeq; ++

) {

isConsidered.push_back((nStructs == 0 || dummyCD.

(

, pPDB)) ? 1 : 0);

lengths.push_back(tmpSeqs.back().length());

(lengths.back() > maxLen) maxLen = lengths.back();

nAlignedBySeq.resize(nSeq);

nGapsBySeq.resize(nSeq);

nAlignedByCol.resize(maxLen);

(j = 0; j < maxLen; ++j) {

(

= 0;

< nSeq; ++

) {

(isConsidered[

] > 0 && j < lengths[

] &&

((

) tmpSeqs[

][j])) {

firstCommon = maxLen - 1;

(

= (nStructs > 0) ? nStructs : nSeq;

> 1 && lastCommon < firstCommon; --

) {

(j < maxLen && nAlignedByCol[j] <

) {

(j > 0 && nAlignedByCol[j - 1] <

) {

(lastCommon <= firstCommon) {

cout <<

<< firstCommon <<

<< lastCommon-1 <<

<<

+1 <<

<< nSeq <<

;

(nStructs > 0) cout <<

;

(j = firstCommon; j < lastCommon; ++j) {

alignedSeqs.

();

(

= 0;

< nSeq; ++

) {

(isConsidered[

] > 0 && j < lengths[

]) {

(

((

) tmpSeqs[

][j])) {

(nAlignedByCol[j] > 1) {

alignedSeqsIt != alignedSeqs.

(); ++alignedSeqsIt) {

++nAlignedBySeq[*alignedSeqsIt];

(

= 0;

< nSeq; ++

) {

(isConsidered[

] == 0)

;

(nAlignedBySeq[

] > nAlignedMax) {

alignedSeqs.

();

nAlignedMax = nAlignedBySeq[

];

(

<<

<<

<< nAlignedMax <<

);

}

(nAlignedBySeq[

] == nAlignedMax) {

(

<<

<<

<< nAlignedMax <<

);

(

<< alignedSeqs.

() <<

<< tmpSeqs.size());

(alignedSeqs.

() == 1) {

}

(alignedSeqs.

() > 1) {

nGapsMin = 1000000000;

alignedSeqsIt != alignedSeqs.

(); ++alignedSeqsIt) {

nGaps = nGapsBySeq[*alignedSeqsIt];

(nGaps < nGapsMin) {

masterIndex = *alignedSeqsIt;

cout <<

<<

<< endl;

(

<<

<<

);

inBlock =

, forcedNewBlock =

;

,

= counts.size();

start = 0;

blockId = 0;

(

= 0;

<

;

++)

(counts[

] >= threshold)

forcedNewBlock = (

> 0 && forcedBreak.

(

-1) != setEnd);

(counts[

] < threshold)

starts.push_back(start);

lengths.push_back(

- start);

}

(forcedNewBlock) {

starts.push_back(start);

lengths.push_back(

- start);

starts.push_back(start);

lengths.push_back(

- start);

starts.size();

originalSequence;

newLength = originalSequence.length();

bioseq.

().SetLength(newLength);

(

= 0;

< nSeq; ++

) {

,

;

longestSequenceIndex = 0;

(

= 0;

< nSeq; ++

) {

(

<<

+1 <<

<<

<<

<< maxLen);

longestSequenceIndex =

;

cerr <<

<<

<<

<< maxLen <<

<< dummyCD.

(

) <<

<< s << endl;

j, masterStart, slaveStart;

nBlocks = blockStarts.

();

(masterSequence.length() == 0 || slaveSequence.length() == 0)

;

(masterSeqid.

() || slaveSeqid.

())

;

(nBlocks != blockLengths.size())

;

(pairwiseSA.

()) {

(pairwiseSA.

()) {

TDD& ddl = pairwiseSA->

().SetDendiag();

(j = 0; j < nBlocks; ++j) {

masterCopy->Assign(*masterSeqid);

slaveCopy->

(*slaveSeqid);

ids.push_back(masterCopy);

ids.push_back(slaveCopy);

masterStart = blockStarts[j] - nGapsPriorToBlockStartMaster[blockStarts[j]];

slaveStart = blockStarts[j] - nGapsPriorToBlockStart[blockStarts[j]];

dd->SetStarts().push_back(masterStart);

dd->SetStarts().push_back(slaveStart);

dd->SetLen(blockLengths[j]);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void remove_if(Container &c, Predicate *__pred)

TGi GetGIFromSequenceList(int SeqIndex) const

int Num3DAlignments() const

string GetSequenceStringByIndex(int SeqIndex)

bool GetSeqIDForIndex(int SeqIndex, CRef< CSeq_id > &SeqID) const

void SetAccession(string Accession, int Version)

int GetNumSequences() const

bool GetPDB(int Row, const CPDB_seq_id *&pPDB)

const CRef< CSeq_entry > & GetSeqEntry() const

virtual bool ReadFile(CNcbiIstream &iStream)=0

bool BuildMasterSlaveSeqAlign(const CRef< CSeq_id > &masterSeqid, const CRef< CSeq_id > &slaveSeqid, const string &masterSequence, const string &slaveSequence, const vector< unsigned int > &blockStarts, const vector< unsigned int > &blockLengths, CRef< CSeq_align > &pairwiseSA)

static unsigned int GetBlocksFromCounts(unsigned int threshold, const vector< unsigned int > &counts, const set< unsigned int > &forcedBreak, vector< unsigned int > &starts, vector< unsigned int > &lengths)

string GetSequence(unsigned int index) const

bool m_preferStructureMaster

static bool PurgeNonAlphaFromSequence(CBioseq &bioseq)

unsigned int DetermineMasterIndex(CCdCore &dummyCD, MasteringMethod masterMethod)

@ eMostAlignedAndFewestGaps

bool MakeAsIsSeqAnnot(CCdCore &dummyCD)

virtual bool IsSeqAnnotValid() const

void PurgeNonAlphaFromCachedSequences()

CRef< CSeq_annot > m_seqAnnot

vector< string > m_sequences

static bool isNotAlpha(char c)

CSeqAnnotFromFasta(bool doIbm=true, bool preferStructureMaster=false, bool caseSensitive=false)

bool MakeIBMSeqAnnot(CCdCore &dummyCD)

void CacheSequences(CCdCore &dummyCD, unsigned int &longestSequenceIndex, bool degapSequences)

virtual bool MakeSeqAnnotFromFasta(CNcbiIstream &is, CFastaIOWrapper &fastaIO, MasteringMethod masterMethod, unsigned int masterIndex=(unsigned int) eUnassignedMaster)

static void CountNonAlphaToPositions(const vector< unsigned int > &positions, const string &sequence, map< unsigned int, unsigned int > &numNonAlpha)

unsigned int m_masterIndex

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

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

bool PurgeNonAlpha(string &s)

void NcbistdaaToNcbieaaString(const vector< char > &vec, string *str)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

void SetId(TId &value)

Assign a value to Id data member.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

TGid & SetGid(void)

Select the variant.

void SetSequences(TSequences &value)

Assign a value to Sequences data member.

void SetName(const TName &value)

Assign a value to Name data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

vector< CRef< CSeq_id > > TIds

list< CRef< CDense_diag > > TDendiag

@ eType_partial

mapping pieces together

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

TNcbieaa & SetNcbieaa(void)

Select the variant.

list< CRef< CSeq_align > > TAlign

void SetInst(TInst &value)

Assign a value to Inst data member.

TNcbistdaa & SetNcbistdaa(void)

Select the variant.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

TIupacaa & SetIupacaa(void)

Select the variant.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

unsigned int

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

The NCBI C++/STL use hints.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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