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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alignment__set_8cpp_source.html below:

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

63 if

(!master || !parentSet->sequenceSet) {

64 ERRORMSG

(

"AlignmentSet::AlignmentSet() - need sequenceSet and master before parsing alignments"

);

69

CSeq_annot::C_Data::TAlign::const_iterator

70 a

, ae = seqAnnots.front()->GetData().GetAlign().end();

71 for

(

=seqAnnots.front()->GetData().GetAlign().begin();

!=ae; ++

)

73 TRACEMSG

(

"number of alignments: "

<< alignments.size());

86 for

(

unsigned int i

=0;

<rowOrder.size(); ++

) rowCheck[rowOrder[

]] =

;

87 if

(rowOrder.size() != multiple->

NRows

() || rowCheck.

size

() != multiple->

NRows

() || rowOrder[0] != 0) {

88 ERRORMSG

(

"AlignmentSet::CreateFromMultiple() - bad row order vector"

);

98

seqAligns.resize((multiple->

NRows

() == 1) ? 1 : multiple->

NRows

() - 1);

99

CSeq_annot::C_Data::TAlign::iterator sa = seqAligns.begin();

106 if

(multiple->

NRows

() > 1) {

108 for

(

unsigned int row

=1;

row

<multiple->

NRows

(); ++

row

, ++sa) {

109

newRow = rowOrder[

row

];

116

unique_ptr<AlignmentSet> newAlignmentSet;

119

}

catch

(exception& e) {

121 "AlignmentSet::CreateFromMultiple() - failed to create AlignmentSet from new asn object; " 122

"exception: "

<< e.what());

127 return

newAlignmentSet.release();

134 const

ncbi::objects::CSeq_align& seqAlign) :

142 const CSeq_id

& frontSeqId = seqAlign.GetSegs().IsDendiag() ?

143

seqAlign.GetSegs().GetDendiag().front()->GetIds().front().GetObject() :

144

seqAlign.GetSegs().GetDenseg().GetIds().front().GetObject();

145 const CSeq_id

& backSeqId = seqAlign.GetSegs().IsDendiag() ?

146

seqAlign.GetSegs().GetDendiag().front()->GetIds().back().GetObject() :

147

seqAlign.GetSegs().GetDenseg().GetIds().back().GetObject();

149 bool

masterFirst =

true

;

150

SequenceSet::SequenceList::const_iterator

154

(*s)->identifier->MatchesSeqId(backSeqId)) {

156

}

else if

((*s)->identifier->MatchesSeqId(frontSeqId) &&

158

masterFirst =

false

;

163 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - couldn't find matching sequences; " 165

<< backSeqId.

AsFastaString

() <<

" must be in the sequence list for this file!"

);

171 unsigned int i

, blockNum = 0;

172 int

masterRes, dependentRes;

175 if

(seqAlign.GetSegs().IsDendiag()) {

177

CSeq_align::C_Segs::TDendiag::const_iterator d , de = seqAlign.GetSegs().GetDendiag().end();

178 for

(d=seqAlign.GetSegs().GetDendiag().begin(); d!=de; ++d, ++blockNum) {

182 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - \n" 183 "incorrect dendiag block dimensions"

);

194 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - " 195 "mismatched Seq-id in dendiag block"

);

200 for

(

=0;

<block.

GetLen

(); ++

) {

203

dependentRes = block.

GetStarts

().back() +

;

206

dependentRes = block.

GetStarts

().front() +

;

208 if

(masterRes < 0 || masterRes >= (

int

)

master

Length

() || dependentRes < 0 || dependentRes >= (

int

)

dependent

Length

()) {

209 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - seqloc in dendiag block > length of sequence!"

);

219 else if

(seqAlign.GetSegs().IsDenseg()) {

221 const CDense_seg

& block = seqAlign.GetSegs().GetDenseg();

224

block.

GetIds

().size() != 2 ||

227 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - \n" 228 "incorrect denseg block dimension"

);

239 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - \n" 240 "mismatched Seq-id in denseg block"

);

245

CDense_seg::TStarts::const_iterator starts = block.

GetStarts

().begin();

246

CDense_seg::TLens::const_iterator lens,

= block.

GetLens

().end();

247 for

(lens=block.

GetLens

().begin(); lens!=

; ++lens) {

249

masterRes = *(starts++);

250

dependentRes = *(starts++);

252

dependentRes = *(starts++);

253

masterRes = *(starts++);

255 if

(masterRes != -1 && dependentRes != -1) {

258 ERRORMSG

(

"MasterDependentAlignment::MasterDependentAlignment() - \n" 259 "seqloc in denseg block > length of sequence!"

);

262 for

(

=0;

<*lens; ++

) {

User-defined methods of the data storage class.

list< const CSeq_align * > SeqAlignList

AlignmentSet(SequenceSet *seqSet, const SeqAnnotList &seqAnnots, bool ignoreBadPairwiseAlignments=false)

SeqAnnotList * newAsnAlignmentData

std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList

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

const Sequence * GetMaster(void) const

std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList

void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const

unsigned int NRows(void) const

MasterDependentAlignment(StructureBase *parent, const Sequence *masterSequence, const ncbi::objects::CSeq_align &seqAlign)

ResidueVector masterToDependent

const Sequence * dependent

ResidueVector blockStructure

bool MatchesSeqId(const ncbi::objects::CSeq_id &sid) const

const MoleculeIdentifier * identifier

unsigned int Length(void) const

const SequenceSet * sequenceSet

const string AsFastaString(void) const

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TLen GetLen(void) const

Get the Len member data.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_align > > TAlign

The NCBI C++/STL use hints.

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

#define row(bind, expected)

static DP_BlockInfo * blocks

ncbi::objects::CSeq_align * CreatePairwiseSeqAlignFromMultipleRow(const BlockMultipleAlignment *multiple, const BlockMultipleAlignment::UngappedAlignedBlockList &blocks, unsigned int slaveRow)

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