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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cav__alignset_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/cddalignview/cav_alignset.cpp Source File

54 #define NCBI_USE_ERRCODE_X Objtools_CAV_Alnset 69

SeqAnnotList::const_iterator

= seqAnnots.end();

70 for

(

=seqAnnots.begin();

; ++

) {

72 if

->GetObject().GetData().IsAlign()) {

73 ERR_POST_X

(1,

Error

"AlignmentSet::AlignmentSet() - confused by alignment data format"

);

77

CSeq_annot::C_Data::TAlign::const_iterator

78 a

, ae =

->GetObject().GetData().GetAlign().end();

79 for

(

->GetObject().GetData().GetAlign().begin();

!=ae; ++

) {

83

!((*a)->GetSegs().IsDendiag() || (*a)->GetSegs().IsDenseg()) ||

84

!(((*a)->IsSetDim() && (*a)->GetDim() == 2) ||

85

((*a)->GetSegs().IsDenseg() && (*a)->GetSegs().GetDenseg().GetDim() == 2)))

87 ERR_POST_X

(2,

Error

"AlignmentSet::AlignmentSet() - confused by alignment type or dimensionality"

);

91

seqaligns.push_back(

->GetPointer());

94 if

(seqaligns.size() == 0) {

95 ERR_POST_X

(3,

Error

"AlignmentSet::AlignmentSet() - no valid Seq-aligns present"

);

103

SeqAlignList::const_iterator

, ae = seqaligns.end();

104 for

(

=seqaligns.begin();

!=ae; ++

) {

105 const SeqIdList

& sids = (*a)->GetSegs().IsDendiag() ?

106

(*a)->GetSegs().GetDendiag().front()->GetIds() :

107

(*a)->GetSegs().GetDenseg().GetIds();

109

SequenceSet::SequenceList::const_iterator

111 for

(s=sequenceSet->

sequences

.begin(); s!=se; ++s) {

112 if

((*s)->Matches(sids.front().GetObject())) {

119 ERR_POST_X

(4,

Error

"AlignmentSet::AlignmentSet() - master must be first sequence of every alignment"

);

129 ERR_POST_X

(6,

Error

"AlignmentSet::AlignmentSet() - couldn't determine which is master sequence"

);

135

SeqAlignList::const_iterator s, se = seqaligns.end();

137 for

(s=seqaligns.begin(); s!=se; ++s, ++

) {

138

unique_ptr < const MasterSlaveAlignment > alignment(

140 if

(!alignment.get() || alignment->Status() !=

CAV_SUCCESS

) {

141 if

(alignment.get() && ignoreBadPairwiseAlignments) {

144 ERR_POST_X

(7,

Error

"Error parsing master/slave pairwise alignment #"

);

173

SequenceSet::SequenceList::const_iterator

182 bool

masterFirst =

true

;

187 if

((*s)->Matches(sids.back().GetObject())) {

189

}

else if

((*s)->Matches(sids.front().GetObject())) {

190

masterFirst =

false

;

199 ERR_POST_X

(9,

Error

"MasterSlaveAlignment::MasterSlaveAlignment() - \n" 200 "couldn't find matching unaligned slave sequence"

);

208 int

masterRes, slaveRes;

213

CSeq_align::C_Segs::TDendiag::const_iterator d , de = seqAlign.

GetSegs

().

GetDendiag

().end();

218

block.

GetIds

().size() != 2 ||

220 ERR_POST_X

(10,

Error

"MasterSlaveAlignment::MasterSlaveAlignment() - \n" 221 "incorrect dendiag block dimensions"

);

228

!slave->Matches(block.

GetIds

().back().GetObject()))) ||

231

!slave->Matches(block.

GetIds

().front().GetObject())))) {

232 ERR_POST_X

(11,

Error

"MasterSlaveAlignment::MasterSlaveAlignment() - \n" 233 "mismatched Seq-id in dendiag block"

);

238 for

(

=0;

<block.

GetLen

(); ++

) {

246 if

(masterRes >= (

int

)

master

Length

() || slaveRes >= (

int

) slave->Length()) {

248 "seqloc in dendiag block > length of sequence!"

);

251

masterToSlave[masterRes] = slaveRes;

262

block.

GetIds

().size() != 2 ||

266 ERR_POST_X

(13,

Error

"MasterSlaveAlignment::MasterSlaveAlignment() - \n" 267 "incorrect denseg block dimension"

);

274

!slave->Matches(block.

GetIds

().back().GetObject()))) ||

277

!slave->Matches(block.

GetIds

().front().GetObject())))) {

278 ERR_POST_X

(14,

Error

"MasterSlaveAlignment::MasterSlaveAlignment() - \n" 279 "mismatched Seq-id in denseg block"

);

284

CDense_seg::TStarts::const_iterator starts = block.

GetStarts

().begin();

285

CDense_seg::TLens::const_iterator lens,

= block.

GetLens

().end();

286 for

(lens=block.

GetLens

().begin(); lens!=

; ++lens) {

288

masterRes = *(starts++);

289

slaveRes = *(starts++);

291

slaveRes = *(starts++);

292

masterRes = *(starts++);

294 if

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

296

(slaveRes + *lens - 1) >= slave->Length()) {

298 "seqloc in denseg block > length of sequence!"

);

301 for

(

=0;

<*lens; ++

)

302

masterToSlave[masterRes +

] = slaveRes +

;

User-defined methods of the data storage class.

list< const CSeq_align * > SeqAlignList

vector< CRef< CSeq_id > > SeqIdList

C interface header for cddalignview as function call.

#define CAV_ERROR_ALIGNMENTS

#define CAV_ERROR_PAIRWISE

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

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

MasterSlaveAlignment(const SequenceSet *sequenceSet, const Sequence *masterSequence, const objects::CSeq_align &seqAlign)

bool Matches(const objects::CSeq_id &seqID) const

unsigned int Length(void) const

string GetTitle(void) const

CConstRef< objects::CBioseq > bioseqASN

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Critical(CExceptionArgs_Base &args)

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetDim(void) const

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

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.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

TDim GetDim(void) const

Get the Dim member data.

const TDendiag & GetDendiag(void) const

Get the variant 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.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

@ eType_partial

mapping pieces together

@ eType_diags

unbroken, but not ordered, diagonals

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

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

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