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NCBI C++ ToolKit: src/app/cn3d/alignment_manager.cpp Source File

originalMultiple =

;

UpdateAlignList::const_iterator u, ue = updates.end();

(u=updates.begin(); u!=ue; ++u) {

(u->GetObject().IsSetSeqannot() && u->GetObject().GetSeqannot().GetData().IsAlign()) {

CSeq_annot::C_Data::TAlign::const_iterator

s, se = u->GetObject().GetSeqannot().GetData().GetAlign().end();

(s=u->GetObject().GetSeqannot().GetData().GetAlign().begin(); s!=se; ++s) {

}

(updateAlignments.size() > 0) {

master = updateAlignments.front()->GetMaster();

SequenceSet::SequenceList::const_iterator q, qe = sSet->

.end();

(q=sSet->

.begin(); q!=qe; ++q) {

((*q)->identifier->MatchesSeqId(

(*s)->GetSegs().IsDendiag() ?

(*s)->GetSegs().GetDendiag().front()->GetIds().front().GetObject() :

(*s)->GetSegs().GetDenseg().GetIds().front().GetObject()

(

<<

);

pairwise.front() = alignment;

updateAlignments.push_back(multiple);

vector < unsigned int >& rowOrder)

(newAlignmentSet) {

(

<<

);

(

);

&currentPSSM = multiple->

().GetPSSM();

(

);

(originalPSSM.

().

() != currentPSSM.GetPssm().GetNumRows() ||

originalPSSM.

().

() != currentPSSM.GetPssm().GetByRow() ||

CPssmFinalData::TScores::const_iterator

c = currentPSSM.GetPssm().GetFinalData().GetScores().begin();

(; o!=oe; ++o, ++c) {

((currentAlignments.size() > 0) ? currentAlignments.front() :

);

AlignmentManager::PairwiseAlignmentList::const_iterator

, ae = alignments.end();

(

=alignments.begin();

!=ae; ++

) {

((*a)->masterToDependent[masterResidue] == -1)

;

AlignmentManager::PairwiseAlignmentList::const_iterator

, ae = alignments.end();

(

=alignments.begin();

!=ae; ++

) {

(((*a)->masterToDependent[masterTo] - (*a)->masterToDependent[masterFrom]) != (masterTo - masterFrom))

AlignmentManager::PairwiseAlignmentList::const_iterator

, ae = alignments.end();

(

=alignments.begin();

!=ae; ++

) {

((*a)->blockStructure[masterTo] != (*a)->blockStructure[masterFrom])

PairwiseAlignmentList::const_iterator

, ae = alignments.end();

BlockMultipleAlignment::SequenceList::iterator s = sequenceList->begin();

*(s++) = alignments.front()->master;

(

=alignments.begin();

!=ae; ++

) {

*(s++) = (*a)->dependent;

((*a)->master != sequenceList->front()) {

(

<<

);

masterFrom = 0, masterTo;

(masterFrom < (

)multipleAlignment->

()->

()) {

(masterTo=masterFrom+1;

newBlock->

= masterTo - masterFrom + 1;

(

=alignments.begin(),

=1;

!=ae; ++

, ++

) {

(*a)->masterToDependent[masterFrom],

(*a)->masterToDependent[masterTo]);

masterFrom = masterTo + 1;

(

);

multipleAlignment;

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator&

,

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator& be,

= 0, c, highlighted = 0;

(;

!=be; ++

) {

range = (*b)->GetRangeOfRow(

);

(c=0; c<(*b)->width; ++c, ++

) {

seqIndexes[

] = range->

+ c;

(countHighlights) {

(

()->IsHighlighted(multiple->GetSequenceOfRow(

), seqIndexes[

]))

seqIndexes[

] = -1;

(!multiple)

;

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

, be =

.end();

(

=

.begin();

!=be; ++

)

nResidues += (*b)->width;

(nResidues == 0) {

(

);

*masterMol, *dependentMol;

(!masterSeq || !(masterMol = masterSeq->

)) {

(

);

*masterSeqIndexes =

[nResidues], *dependentSeqIndexes =

[nResidues];

((highlightedOnly ? nHighlightedAligned : nResidues) < 3) {

(

);

[] masterSeqIndexes;

[] dependentSeqIndexes;

*weights =

[nResidues];

* CVP;

CVP *masterCoords =

CVP[nResidues], *dependentCoords =

CVP[nResidues];

(!masterMol->

(nResidues, masterSeqIndexes, masterCoords)) {

(

);

nStructureAlignments = 0;

(

=1;

<multiple->

(); ++

) {

(!dependentSeq || !(dependentMol = dependentSeq->molecule))

;

(dependentMol->

(nResidues, dependentSeqIndexes, dependentCoords) < 3) {

(

<< dependentSeq->identifier->pdbID <<

);

(

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

(!masterCoords[j] || !dependentCoords[j] || (highlightedOnly && masterSeqIndexes[j] < 0)) {

(

<< (

+1) <<

);

(

<< dependentSeq->identifier->pdbID <<

<< masterSeq->

->

<<

<< nWeighted <<

);

(

*

(dependentObj))->RealignStructure(nResidues, masterCoords, dependentCoords, weights,

);

++nStructureAlignments;

[] masterSeqIndexes;

[] dependentSeqIndexes;

[] masterCoords;

[] dependentCoords;

(*sequences)[

] = (*a)->dependent;

(

);

AlignmentSet::AlignmentList::const_iterator

((*a)->master->molecule) {

((*a)->master->molecule->GetParentOfType(&

))

(

=0;

!=ae; ++

, ++

) {

((*a)->dependent->molecule) {

((*a)->dependent->molecule->GetParentOfType(&

))

(

);

(visibilities[

])

alignments.push_back(*

);

(!sequence)

;

(currentAlignment)

currentAlignment->

(sequence, seqIndex);

(!sequence)

;

(currentAlignment) {

((*(currentAlignment->

()))[

] == sequence)

(currentAlignment)

(

);

(dependentsToRealign.size() == 0)

;

(multiple->

(dependentsToRealign, &alignments)) {

(

);

(currentAlignments.size() == 0)

;

nRowsAddedToMultiple;

foundSingle =

;

singleList.push_back(single);

options, currentAlignments.front(), &singleList, &newAlignments, &nRowsAddedToMultiple,

)) {

Threader::AlignmentList::const_iterator

,

= newAlignments.end();

(

=newAlignments.begin();

!=

; ++

)

replacedList.push_back(*

);

replacedList.push_back((*a)->Clone());

);

(nRowsAddedToMultiple > 0)

(currentAlignments.size() == 0)

;

nRowsAddedToMultiple;

(nRowsAddedToMultiple > 0)

RowsAdded(nRowsAddedToMultiple, currentAlignments.front());

(updatesToMerge.size() == 0)

;

(currentUpdates.size() == 0)

;

ViewerBase::AlignmentList::const_iterator u, ue = currentUpdates.end();

(u=currentUpdates.begin(); u!=ue; ++u) {

(updatesToMerge.find(*u) != updatesToMerge.end()) {

vector < unsigned int > rowOrder(newMultiple->

());

(

=0;

<newMultiple->

(); ++

) rowOrder[

] =

;

(

);

nSuccessfulMerges = 0;

(u=currentUpdates.begin(); u!=ue; ++u) {

(*u == newMultiple)

;

merged =

;

(updatesToMerge.find(*u) != updatesToMerge.end()) {

nSuccessfulMerges += (*u)->NRows() - 1;

(

=0;

<(*u)->NRows(); ++

) {

status = (*u)->GetRowStatusLine(

);

(status.size() > 0)

status +=

;

status =

;

(*u)->SetRowStatusLine(

, status);

updatesToKeep.push_back(keep);

(nSuccessfulMerges > 0) {

(mergeToNeighbor && nSuccessfulMerges == 1) {

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

, be =

.end();

rowScore, bestScore = 0;

col,

, lastRow = multiple->

() - 1;

(

=

.begin();

!=be; ++

) {

(col=0; col<(*b)->width; ++col) {

mergeSeq->

[(*b)->GetRangeOfRow(lastRow)->from + col],

(

== 0 || rowScore > bestScore) {

bestScore = rowScore;

(

<< (where+1) <<

updateSequences->clear();

(currentUpdates.size() == 0)

;

ViewerBase::AlignmentList::const_iterator u, ue = currentUpdates.end();

(u=currentUpdates.begin(); u!=ue; ++u)

updateSequences->push_back((*u)->GetSequenceOfRow(1));

(chains->size() > 0);

(

);

(!multiple)

;

vector < unsigned int > rowsToRemove;

(

=1;

<multiple->

(); ++

)

rowsToRemove.push_back(

);

(rowsToRemove.size() > 0) {

(

);

(

);

(currentUpdates.size() == 0)

;

ViewerBase::AlignmentList::const_iterator u, ue = currentUpdates.end();

(u=currentUpdates.begin(); u!=ue; ++u)

((*u)->GetSequenceOfRow(1)->identifier == identifier)

;

(u=currentUpdates.begin(); u!=ue; ++u) {

((*u)->GetSequenceOfRow(1)->identifier != identifier) {

updatesToKeep.push_back(keep);

(!currentMultiple)

;

(currentUpdates.size() == 0)

nRowsAddedToMultiple;

currentUpdates, &newAlignmentsList, &nRowsAddedToMultiple,

)) {

(nRowsAddedToMultiple > 0)

(!currentMultiple)

;

nRowsAddedToMultiple;

foundSingle =

;

singleList.push_back(single);

currentMultiple, singleList, &newAlignments, &nRowsAddedToMultiple,

)) {

BlockAligner::AlignmentList::const_iterator

,

= newAlignments.end();

(

=newAlignments.begin();

!=

; ++

)

replacedList.push_back(*

);

replacedList.push_back((*a)->Clone());

);

(nRowsAddedToMultiple > 0)

anyChanges =

;

newAlignments->clear();

UpdateViewer::AlignmentList::const_iterator

, te = toExtend.end();

(

=toExtend.begin();

!=te; ++

) {

newAlignments->push_back(p);

(pairBlocks.size() == 0)

list < ExtendInfo > ExtendList;

ExtendMap extendMap;

(

mb=0; mb<multBlocks.size(); ++mb) {

*multRange = multBlocks[mb]->GetRangeOfRow(0);

(

=0;

<pairBlocks.size(); ++

) {

*pairRange = pairBlocks[

]->GetRangeOfRow(0);

(pairRange->

> multRange->

&& pairRange->

<= multRange->

&&

ExtendList& el = extendMap[ub];

el.resize(el.size() + 1);

el.back().multBlock = mb;

el.back().pairBlock =

;

el.back().extendPairBlockLeft =

;

el.back().nResidues = pairRange->

- multRange->

;

(

<< (

+1) <<

);

(pairRange->

< multRange->

&& pairRange->

>= multRange->

&&

ExtendList& el = extendMap[ub];

el.resize(el.size() + 1);

el.back().multBlock = mb;

el.back().pairBlock =

;

el.back().extendPairBlockLeft =

;

el.back().nResidues = multRange->

- pairRange->

;

(

<< (

+1) <<

);

ExtendMap::const_iterator u, ue = extendMap.end();

(u=extendMap.begin(); u!=ue; ++u) {

(u->second.size() == 2 && (u->second.back().multBlock - u->second.front().multBlock > 1)) {

(

<< (u->second.front().pairBlock+1) <<

<< (u->second.back().pairBlock+1));

ExtendList::const_iterator e, ee;

(u->first->MinResidues() == u->first->width && u->second.size() == 2 &&

u->second.front().multBlock == u->second.back().multBlock)

ExtendList& modList =

ExtendList&

(u->second);

modList.front().nResidues = u->first->width;

modList.erase(++(modList.begin()));

= u->first->MinResidues(), totalShifts = 0;

(e=u->second.begin(), ee=u->second.end(); e!=ee; ++e)

totalShifts += e->nResidues;

(

<< (u->second.front().extendPairBlockLeft ?

:

)

<<

<< (u->second.front().pairBlock+1) <<

);

(e=u->second.begin(), ee=u->second.end(); e!=ee; ++e) {

(e->extendPairBlockLeft ?

pairBlocks[e->pairBlock]->GetRangeOfRow(0)->from :

pairBlocks[e->pairBlock]->GetRangeOfRow(0)->to),

(

<< (e->extendPairBlockLeft ?

:

)

<<

<< (e->pairBlock+1) <<

<< e->nResidues <<

);

(p->

(alnIdx, alnIdx + (e->extendPairBlockLeft ? -e->nResidues : e->nResidues)))

(

);

vector < int > mergeIndexes;

(

=0;

<pairBlocks.size(); ++

) {

*pairRange = pairBlocks[

]->GetRangeOfRow(0);

(prevRange && prevRange->

== pairRange->

- 1 && multiple.

(0

, prevRange->

)) {

(pAlnIdx1 == pAlnIdx2 - 1 &&

(

<<

<<

<< (

+1));

mergeIndexes.push_back(pAlnIdx1);

prevRange = pairRange;

(

=0;

<mergeIndexes.size(); ++

) {

(p->

(mergeIndexes[

], mergeIndexes[

] + 1))

(

);

(!currentMultiple)

;

(currentUpdates.size() == 0)

(!currentMultiple)

;

singleList.push_back(single);

(newAlignments.size() != 1) {

(

);

foundSingle =

;

(*

== single) {

replacedList.push_back(newAlignments.front());

foundSingle =

;

replacedList.push_back((*a)->Clone());

(

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static int GetAlignedResidueIndexes(BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator &b, BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator &be, int row, int *seqIndexes, bool countHighlights=false, const BlockMultipleAlignment *multiple=NULL)

static bool NoBlockBoundariesBetween(int masterFrom, int masterTo, const AlignmentManager::PairwiseAlignmentList &alignments)

static bool AlignedToAllDependents(int masterResidue, const AlignmentManager::PairwiseAlignmentList &alignments)

static bool CreateNewPairwiseAlignmentsByBlockExtension(const BlockMultipleAlignment &multiple, const UpdateViewer::AlignmentList &toExtend, UpdateViewer::AlignmentList *newAlignments)

static bool NoDependentInsertionsBetween(int masterFrom, int masterTo, const AlignmentManager::PairwiseAlignmentList &alignments)

void NewAlignments(const SequenceSet *sSet, const AlignmentSet *aSet)

const SequenceSet * sequenceSet

void BlockAlignUpdate(BlockMultipleAlignment *single)

void ShowSequenceViewer(bool showNow) const

void ExtendAllUpdates(void)

bool IsInAlignment(const Sequence *sequence) const

void RealignAllDependentStructures(bool highlightedOnly) const

AlignmentManager(const SequenceSet *sSet, const AlignmentSet *aSet)

void CalculateRowScoresWithThreader(double weightPSSM)

std::vector< unsigned int > originalRowOrder

void PurgeSequence(const MoleculeIdentifier *identifier)

UpdateViewer * updateViewer

void RealignDependentSequences(BlockMultipleAlignment *multiple, const std::vector< unsigned int > &dependentsToRealign)

BlockMultipleAlignment * CreateMultipleFromPairwiseWithIBM(const PairwiseAlignmentList &alignments)

void BlockAlignAllUpdates(void)

void ExtendUpdate(BlockMultipleAlignment *single)

const Vector * GetAlignmentColor(const Sequence *sequence, unsigned int seqIndex, StyleSettings::eColorScheme colorScheme) const

void ShowHideCallbackFunction(const std::vector< bool > &itemsEnabled)

void ShowUpdateWindow(void) const

virtual ~AlignmentManager(void)

void GetUpdateSequences(std::list< const Sequence * > *updateSequences) const

std::map< BlockMultipleAlignment *, bool > UpdateMap

void GetAlignmentSetDependentVisibilities(std::vector< bool > *visibilities) const

std::list< ncbi::CRef< ncbi::objects::CUpdate_align > > UpdateAlignList

SequenceViewer * sequenceViewer

bool GetStructureProteins(std::vector< const Sequence * > *chains) const

BlockMultipleAlignment * originalMultiple

unsigned int NUpdates(void) const

void ThreadUpdate(const ThreaderOptions &options, BlockMultipleAlignment *single)

void SavePairwiseFromMultiple(const BlockMultipleAlignment *multiple, const std::vector< unsigned int > &rowOrder)

const BlockMultipleAlignment * GetCurrentMultipleAlignment(void) const

std::vector< bool > dependentsVisible

BlockAligner * blockAligner

void ReplaceUpdatesInASN(ncbi::objects::CCdd::TPending &newUpdates) const

bool IsAligned(const Sequence *sequence, unsigned int seqIndex) const

void NewMultipleWithRows(const std::vector< bool > &visibilities)

void MergeUpdates(const UpdateMap &updates, bool mergeToNeighbor)

const AlignmentSet * alignmentSet

std::list< const MasterDependentAlignment * > PairwiseAlignmentList

void GetAlignmentSetDependentSequences(std::vector< const Sequence * > *sequences) const

void ThreadAllUpdates(const ThreaderOptions &options)

static AlignmentSet * CreateFromMultiple(const BlockMultipleAlignment *multiple, SeqAnnotList *newAsnAlignmentData, const SequenceSet &sequenceSet, const std::vector< unsigned int > *rowOrder=NULL)

bool CreateNewPairwiseAlignmentsByBlockAlignment(BlockMultipleAlignment *multiple, const AlignmentList &toRealign, AlignmentList *newAlignments, int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer)

std::list< BlockMultipleAlignment * > AlignmentList

BlockMultipleAlignment * Clone(void) const

std::vector< const Sequence * > SequenceList

const UnalignedBlock * GetUnalignedBlockBefore(const UngappedAlignedBlock *aBlock) const

bool MoveBlockBoundary(unsigned int columnFrom, unsigned int columnTo)

ncbi::CRef< ncbi::objects::CUpdate_align > updateOrigin

const Vector * GetAlignmentColor(const Sequence *sequence, unsigned int seqIndex, StyleSettings::eColorScheme colorScheme) const

const BLAST_Matrix * GetPSSM(void) const

const Sequence * GetMaster(void) const

std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList

void RemovePSSM(void) const

bool ExtractRows(const std::vector< unsigned int > &slavesToRemove, AlignmentList *pairwiseAlignments)

const Sequence * GetSequenceOfRow(unsigned int row) const

unsigned int GetAlignedBlockNumber(unsigned int alignmentIndex) const

void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const

unsigned int GetAlignmentIndex(unsigned int row, unsigned int seqIndex, eUnalignedJustification justification)

unsigned int NRows(void) const

bool HasNoAlignedBlocks(void) const

bool UpdateBlockMapAndColors(bool clearRowInfo=true)

const SequenceList * GetSequences(void) const

bool MergeBlocks(unsigned int fromAlignmentIndex, unsigned int toAlignmentIndex)

bool IsAligned(unsigned int row, unsigned int seqIndex) const

bool AddUnalignedBlocks(void)

bool AddAlignedBlockAtEnd(UngappedAlignedBlock *newBlock)

bool MergeAlignment(const BlockMultipleAlignment *newAlignment)

const UnalignedBlock * GetUnalignedBlockAfter(const UngappedAlignedBlock *aBlock) const

void SetRangeOfRow(unsigned int row, int from, int to)

void PostRedrawMolecule(const Molecule *molecule)

void PostRedrawAllStructures(void)

void UnPostRedrawSequenceViewer(ViewerBase *viewer)

void RemoveSequenceViewer(const ViewerBase *sequenceViewer)

void AddSequenceViewer(ViewerBase *sequenceViewer)

void PostRedrawAllSequenceViewers(void)

static const int VALUE_NOT_SET

std::string ToString(void) const

int GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector **coords) const

void GetProteinSequences(SequenceList *seqs) const

void RowsAdded(unsigned int nRowsAddedToMultiple, BlockMultipleAlignment *multiple, int where=-1)

void RowsRemoved(const std::vector< unsigned int > &rowsRemoved, const BlockMultipleAlignment *multiple)

void CreateSequenceWindow(bool showNow)

void DisplayAlignment(BlockMultipleAlignment *multipleAlignment)

void DisplaySequences(const SequenceList *sequenceList)

const Molecule * molecule

const MoleculeIdentifier * identifier

unsigned int Length(void) const

int GetOrSetMMDBLink(void) const

void Show(const StructureBase *entity, bool isShown)

bool GetParentOfType(const T **ptr, bool warnIfNotFound=true) const

static const unsigned int eRowOrderData

void InitStructureAlignments(int masterMMDBID)

void ReplaceAlignmentSet(AlignmentSet *newAlignmentSet)

void RemoveStructureAlignments(void)

ShowHideManager * showHideManager

void ReplaceUpdates(ncbi::objects::CCdd::TPending &newUpdates)

void SetDataChanged(unsigned int what) const

StyleManager * styleManager

static const unsigned int ePSSMData

std::list< BlockMultipleAlignment * > AlignmentList

bool Realign(const ThreaderOptions &options, BlockMultipleAlignment *masterMultiple, const AlignmentList *originalAlignments, AlignmentList *newAlignments, unsigned int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer)

bool CalculateScores(const BlockMultipleAlignment *multiple, double weightPSSM)

void SavePendingStructures(void)

void ReplaceAlignments(const AlignmentList &alignmentList)

void AddAlignments(const AlignmentList &alignmentList)

std::list< BlockMultipleAlignment * > AlignmentList

void CreateUpdateWindow(void)

void SetInitialState(void)

std::list< BlockMultipleAlignment * > AlignmentList

SequenceDisplay * GetCurrentDisplay(void)

bool EditorIsOn(void) const

const AlignmentList & GetCurrentAlignments(void) const

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

struct parameters_t * pb[]

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDiag_Info

Informational message.

@ eDiag_Warning

Warning message.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

TNumRows GetNumRows(void) const

Get the NumRows member data.

bool IsSetFinalData(void) const

Final representation for the PSSM Check if a value has been assigned to FinalData data member.

TH GetH(void) const

Get the H member data.

TKappa GetKappa(void) const

Get the Kappa member data.

const TScores & GetScores(void) const

Get the Scores member data.

TScalingFactor GetScalingFactor(void) const

Get the ScalingFactor member data.

const TFinalData & GetFinalData(void) const

Get the FinalData member data.

TNumColumns GetNumColumns(void) const

Get the NumColumns member data.

TByRow GetByRow(void) const

Get the ByRow member data.

const TPssm & GetPssm(void) const

Get the Pssm member data.

TLambda GetLambda(void) const

Get the Lambda member data.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are available

if(yy_accept[yy_current_state])

Messenger * GlobalMessenger(void)

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

bool ne(T x_, T y_, T round_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define row(bind, expected)

static DP_BlockInfo * blocks

static int GetBLOSUM62Score(char a, char b)

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