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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuCD_8cpp_source.html below:

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

(!cd->AlignAnnotsValid()) {

list< CRef< CCdd_descr > >& cdDescrList = cd->

().Set();

list< CRef< CCdd_descr > >::iterator lit = cdDescrList.begin();

(lit != cdDescrList.end())

((*lit)->IsRepeats())

lit = cdDescrList.erase(lit);

(!pCD->

() || positions.size() == 0)

list< CRef< CSeq_align > >& alignments = pCD->

();

(alignments.size() != positions.size())

vector<CRef< CSeq_align > > temp(alignments.size());

list<CRef< CSeq_align > >::iterator lit = alignments.begin();

(;lit != alignments.end(); lit++)

(positions[

] >= (

) temp.size())

temp[positions[

]] = *lit;

(

= 0;

< temp.size();

++)

alignments.push_back(temp[

]);

TStructureAlignments::iterator saListIt, saListEnd;

TSAMap::iterator saMapIt, saMapEnd;

(

-1 != positions.size())

TStructureAlignments& saList = pCD->

().SetFeatures().front()->SetFeatures();

saListIt = saList.begin();

saListEnd = saList.end();

(

= 0;

< (

- 1) && saListIt != saListEnd; ++

) {

(nPDBs == n3DAlign) {

saMapIt = saMapTmp.begin();

saMapEnd = saMapTmp.end();

(; saMapIt != saMapEnd; ++saMapIt) {

saList.push_back(saMapIt->second);

list< CRef< CCdd_descr > > & descList = cd->

().Set();

list< CRef< CCdd_descr > >::iterator it = descList.begin();

(; it != descList.end(); it++)

((*it)->IsCreate_date())

dateDesc->SetCreate_date(*curDate);

descList.push_back(dateDesc);

list< CRef< CCdd_descr > > & descList = cd->

().Set();

list< CRef< CCdd_descr > >::iterator it = descList.begin();

(; it != descList.end(); it++)

((*it)->IsUpdate_date())

dateDesc->SetUpdate_date(*curDate);

descList.push_back(dateDesc);

Lower, Upper, Lower2, Upper2;

(

j=0; j<NumMatches; j++) {

(((Lower2 >= Lower) && (Lower2 <= Upper)) ||

((Upper2 >= Lower) && (Upper2 <= Upper)) ||

((Lower2 <= Lower) && (Upper2 >= Upper)) ||

((Lower2 >= Lower) && (Upper2 <= Upper))) {

rows2.push_back(matches[j]);

}

(cd1AsChild) {

((Lower2 >= Lower) && (Upper2 <= Upper)) {

rows2.push_back(matches[j]);

((Lower2 <= Lower) && (Upper2 >= Upper)) {

rows2.push_back(matches[j]);

sameCD = (cd1 == cd2 || !cd2) ?

:

;

(cd1 ==

&& cd2 ==

)

0;

(sameCD && !cd2) {

(RowIndex1=0; RowIndex1<NumRows; RowIndex1++) {

NumMatches =

(cd1, RowIndex1, cd2, matches,

,

);

(sameCD && NumMatches == 1) {

(

j=0; j<NumMatches; j++) {

(sameCD && matches[j] == RowIndex1) {

rowsOfCD1.push_back(RowIndex1);

rowsOfCD2.push_back(matches[j]);

rowsOfCD1.size();

vector<int> rows1, rows2;

(!cd || (convertedSequences.size() > 0 && !forceRecompute)) {

convertedSequences.clear();

(

= 0;

< numSeq; ++

) {

(ppAlignedResidues ==

) {

ppAlignedResidues =

*[numRows];

(

=0;

<numRows;

++) {

ppAlignedResidues[

] =

[numAligned]{ 0 };

}

(!forceRecompute) {

(

= 0;

< numRows;

++) {

isMaster = (

== 0);

isOK =

, useRefRow =

;

, col,

, pos, mapIndex,

, nCols, nBlocks;

** alignedResidues =

;

rowString, colString;

vector<int> starts, lengths;

(

<< cd->

() <<

);

(

<< cd->

() <<

);

(referenceRow >=

) {

nBlocks = starts.size();

(nBlocks == lengths.size()) {

(

= 0, col = 0;

< nBlocks; ++

) {

pos = (useRefRow) ? starts[

] : col;

(j = 0; j < lengths[

]; ++j, ++col, ++pos) {

(isOK && alignedResidues) {

(col = 0; col < nCols; ++col) {

colString += alignedResidues[

][col];

mapIndex = colToPos[col];

[mapIndex] = colString;

(alignedResidues) {

[] alignedResidues[

];

[] alignedResidues;

masterBioseq->

(*bioseq);

list< CRef< CSeq_id > >& idList = masterBioseq->

();

idList.push_back(seqIdRef);

list< CRef< CSeq_annot > >& seqAnnots = masterBioseq->

();

list< CRef< CSeq_loc > >& seqlocs = seqAnnot->

().SetLocs();

seqlocs.push_back(seqLoc);

seqAnnots.push_back(seqAnnot);

+

BioseqForNthRow->

(*bioseq);

(BioseqForNthRow);

BioseqForNthRow->

(*bioseq);

list< CRef< CSeq_id > >& idList = BioseqForNthRow->

();

idList.push_back(seqIdRef);

list< CRef< CSeq_annot > >& seqAnnots = BioseqForNthRow->

();

list< CRef< CSeq_loc > >& seqlocs = seqAnnot->

().SetLocs();

seqlocs.push_back(seqLoc);

seqAnnots.push_back(seqAnnot);

BioseqForNthRow;

(

=0;

<

;

++) {

(!errstr.empty())

(

);

(!taxServer.

())

(

= 0;

< num;

++)

cd->

(

,gi,

);

joined = taxServer.

(comTax, taxid);

(

<<comTax<<

<<taxid<<

);

orgRef->

(*taxServer.

(comTax, is_species, is_uncultured, blast_name));

nAncestors, nClassical = 0;

(

&& isAncestors) {

list< CRef< CDomain_parent > >::const_iterator pit = pCD->

().begin(), pit_end = pCD->

().end();

(pit != pit_end) {

= ((nClassical == 1 && nAncestors == 1) ||

(nClassical == 0 && nAncestors > 0));

* msgHeader =

;

(seqId->

())

(;

< nrows;

++)

(seqId->

())

list<CRef< CSeq_align > >& seqAlignList = cd->

();

list<CRef< CSeq_align > >::iterator lit = seqAlignList.begin();

list<CRef< CSeq_align > >::iterator guideIt;

(; lit != seqAlignList.end(); lit++)

.remaster(guideBmp);

*lit =

.toSeqAlign();

(SeqID->

()) {

((

)oldMasterRow >= cd.

() || oldMasterRow == 0)

;

From, To, NewFrom, NewTo;

CAlign_annot_set::Tdata::iterator alignAnnotIt, alignAnnotEnd;

CPacked_seqint::Tdata::iterator intervalIt, intervalEnd;

(alignAnnotIt = cd.

().Set().begin(); alignAnnotIt != alignAnnotEnd; alignAnnotIt++) {

((*alignAnnotIt)->SetLocation().IsInt()) {

From = (

) (*alignAnnotIt)->SetLocation().GetInt().GetFrom();

To = (

) (*alignAnnotIt)->SetLocation().GetInt().GetTo();

(!seqIdOldMaster->

((*alignAnnotIt)->SetLocation().SetInt().GetId()) || NewFrom < 0 || NewTo < 0)

(seqIdMaster->

((*alignAnnotIt)->SetLocation().SetInt().GetId()) && !seqIdMaster->

(*seqIdOldMaster)) {

(*alignAnnotIt)->SetLocation().SetInt().SetFrom(NewFrom);

(*alignAnnotIt)->SetLocation().SetInt().SetTo(NewTo);

(*alignAnnotIt)->SetLocation().SetInt().SetId(*seqIdMaster);

((*alignAnnotIt)->SetLocation().IsPacked_int()) {

intervalIt = (*alignAnnotIt)->SetLocation().SetPacked_int().Set().begin();

intervalEnd = (*alignAnnotIt)->SetLocation().SetPacked_int().Set().end();

(; intervalIt != intervalEnd; ++intervalIt) {

From = (

) (*intervalIt)->GetFrom();

To = (

) (*intervalIt)->GetTo();

(!seqIdOldMaster->

((*intervalIt)->GetId()) || NewFrom < 0 || NewTo < 0)

(seqIdMaster->

((*intervalIt)->GetId()) && !seqIdMaster->

(*seqIdOldMaster)) {

(*intervalIt)->SetFrom(NewFrom);

(*intervalIt)->SetTo(NewTo);

(*intervalIt)->SetId(*seqIdMaster);

vector<int> consensusRows, consensusSeqListIds;

(

= consensusSeqListIds.size() - 1;

>= 0 ; --

) {

(masterLen == 0)

;

, j, nBlocks;

vector<BlockModelPair*> blockModelPairs;

forcedCTerminiInIntersection;

list< CRef< CSeq_align > >& cdSeqAligns = ccd->

();

list< CRef< CSeq_align > >::iterator cdSeqAlignIt = cdSeqAligns.begin(), cdSeqAlignEnd = cdSeqAligns.end();

(

= 0; cdSeqAlignIt != cdSeqAlignEnd; ++cdSeqAlignIt, ++

) {

(

&&

->isValid()) {

blockModelPairs.push_back(

);

(j = 0; j < nBlocks - 1; ++j) {

forcedCTerminiInIntersection.

(

->getMaster().getBlock(j).getEnd());

(blockModelPairs.size() != cdSeqAligns.size()) {

nAlignedIBM = (intersectedBlockModel) ? intersectedBlockModel->

() : 0;

(nAlignedIBM == 0) {

nBlocks = intersectedBlockModel->

().size();

(

= 0, cdSeqAlignIt = cdSeqAligns.begin();

<

- 1 ; ++

, ++cdSeqAlignIt) {

= blockModelPairs[

];

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

& jthMasterBlock = intersectedBlockModel->

(j);

slaveStart =

->mapToMaster(jthMasterBlock.

());

(slaveStart != -1);

intersectedSeqAlignSlave->

(

);

*cdSeqAlignIt = intersectedSeqAlignSlave->

(*intersectedBlockModel);

blockModelPairs.clear();

intersectedBlockModel;

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.

bool GetSeqIDForRow(int row, CRef< CSeq_id > &SeqID) const

void addOneAlignment(const BlockModel &bm)

BlockModel * getIntersectedAlignment(double rowFraction=1.0)

CRef< CSeq_align > toSeqAlign() const

int mapToMaster(int slavePos) const

int getTotalBlockLength() const

CRef< CSeq_id > getSeqId() const

CRef< CSeq_align > toSeqAlign(const BlockModel &master) const

void addBlock(Block &block)

int getGapToCTerminal(int bn, int len=-1) const

vector< Block > & getBlocks()

bool EraseTheseRows(const std::vector< int > &TossRows)

void EraseSequence(int SeqIndex)

int GetUpperBound(int Row) const

string GetSequenceStringByRow(int rowId)

bool GetSeqAlign(int Row, CRef< CSeq_align > &seqAlign)

int GetRowsWithConsensus(vector< int > &consensusRows) const

bool GetSeqIDFromAlignment(int RowIndex, CRef< CSeq_id > &SeqID) const

bool FindConsensusInSequenceList(vector< int > *indices=NULL) const

int Num3DAlignments() const

string GetSequenceStringByIndex(int SeqIndex)

int GetAllRowIndicesForSeqId(const CRef< CSeq_id > &SeqID, list< int > &rows) const

int GetAlignmentLength() const

int GetLowerBound(int Row) const

const list< CRef< CSeq_align > > & GetSeqAligns() const

bool UsesConsensusSequenceAsMaster() const

bool GetGI(int Row, TGi &GI, bool ignorePDBs=true)

bool GetBioseqForRow(int rowId, CRef< CBioseq > &bioseq)

string GetAccession(int &Version) const

int GetNumSequences() const

bool GetSeqIDForRow(int Pair, int DenDiagRow, CRef< CSeq_id > &SeqID) const

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

bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)

CConstRef< COrg_ref > GetOrgRef(TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name, bool *is_specified=NULL)

TTaxId Join(TTaxId taxid1, TTaxId taxid2)

bool isBlockAligned() const

iterator_bool insert(const value_type &val)

void SetAlignedResiduesOnSequence(const CRef< CSeq_align > &align, const string &sequenceString, char *&pAlignedRes, bool isMaster=false)

int GetBlockLengths(const CRef< CSeq_align > &seqAlign, vector< int > &lengths)

int GetBlockStarts(const CRef< CSeq_align > &seqAlign, vector< int > &starts, bool onMaster)

bool SetCreationDate(CCdCore *cd)

bool ReMasterCdWithoutUnifiedBlocks(CCdCore *cd, int Row, bool resetFields)

int NumberOfOverlappedRows(CCdCore *cd1, CCdCore *cd2)

bool RemasterWithStructure(CCdCore *cd, string *msg)

void ResetFields(CCdCore *cd)

CCdCore * CopyCD(const CCdCore *cd)

bool obeysParentTypeConstraints(const CCdCore *pCD)

int GetOverlappedRows(CCdCore *cd1, CCdCore *cd2, vector< int > &rowsOfCD1, vector< int > &rowsOfCD2)

int PurgeConsensusSequences(CCdCore *pCD, bool resetFields)

string GetVerboseNameStr(const CCdCore *cd)

void SetAlignedResiduesForCD(CCdCore *cd, char **&ppAlignedResidues, bool forceRecompute)

bool Reorder(CCdCore *pCD, const vector< int > positions)

CRef< COrg_ref > GetCommonTax(CCdCore *cd, bool useRootWhenNoTaxInfo)

CCdCore * ExtractCDFromMime(CNcbi_mime_asn1 *ncbiMime)

bool remasterAlignannot(CCdCore &cd, unsigned int oldMasterRow)

void GetAlignmentColumnsForCD(CCdCore *cd, map< unsigned int, string > &columns, unsigned int referenceRow)

CRef< CBioseq > GetMasterBioseqWithFootprintOld(CCdCore *cd)

bool ReorderStructureAlignments(CCdCore *pCD, const vector< int > &positions)

bool SetUpdateDate(CCdCore *cd)

bool GetBioseqWithFootprintForNRows(CCdCore *cd, int N, vector< CRef< CBioseq > > &bioseqs, string &errstr)

int GetMappedRowIds(CCdCore *cd1, int row1, CCdCore *cd2, vector< int > &rows2, bool cd1AsChild, bool overlapMode)

void SetConvertedSequencesForCD(CCdCore *cd, vector< string > &convertedSequences, bool forceRecompute)

int IntersectByMaster(CCdCore *ccd, double rowFraction)

CRef< CBioseq > GetBioseqWithFootprintForNthRow(CCdCore *cd, int N, string &errstr)

CRef< CBioseq > GetMasterBioseqWithFootprint(CCdCore *cd)

int GetReMasterFailureCode(const CCdCore *cd)

const int ALIGN_ANNOTS_VALID_FAILURE

static ASNClass * CopyASNObject(const ASNClass &originalObject, std::string *err)

TTaxId GetTaxIdInBioseq(const CBioseq &bioseq)

static const char si[8][64]

thread_local unique_ptr< FtaMsgPost > bmp

static const column_t columns[]

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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

Set object to copy of another one.

const string AsFastaString(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

void Reset(void)

Reset reference object.

#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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ eCurrent

Use current time. See also CCurrentTime.

list< CRef< CBiostruc_feature > > TFeatures

const TFeatures & GetFeatures(void) const

Get the Features member data.

void ResetTrunc_master(void)

Reset Trunc_master data member.

void ResetFeatures(void)

Reset Features data member.

TMaster3d & SetMaster3d(void)

Assign a value to Master3d data member.

void ResetScoremat(void)

Reset Scoremat data member.

bool IsSetAlignannot(void) const

alignment annotation Check if a value has been assigned to Alignannot data member.

void ResetProfile_range(void)

Reset Profile_range data member.

void SetFeatures(TFeatures &value)

Assign a value to Features data member.

void SetDescription(TDescription &value)

Assign a value to Description data member.

const TAncestors & GetAncestors(void) const

Get the Ancestors member data.

void ResetDistance(void)

Reset Distance data member.

bool IsSetMaster3d(void) const

record if CD has a 3D representative Check if a value has been assigned to Master3d data member.

bool IsSetAncestors(void) const

list of parents Check if a value has been assigned to Ancestors data member.

void SetAlignannot(TAlignannot &value)

Assign a value to Alignannot data member.

void ResetPosfreq(void)

Reset Posfreq data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSetParent(void) const

this CD is the result of a split Check if a value has been assigned to Parent data member.

bool IsSetFeatures(void) const

contains structure alignment data or "core" definitions Check if a value has been assigned to Feature...

const TFeatures & GetFeatures(void) const

Get the Features member data.

@ eParent_type_classical

the classification of parent child relations

bool IsGeneral(void) const

Check if variant General is selected.

const TCdd & GetCdd(void) const

Get the variant data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsCdd(void) const

Check if variant Cdd is selected.

const TSeq_align_data & GetSeq_align_data(void) const

Get the Seq_align_data member data.

bool IsPdb(void) const

Check if variant Pdb is selected.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

unsigned int

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

double value_type

The numeric datatype used by the parser.

Defines: CTimeFormat - storage class for time format.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

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