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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/psl__data_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/psl_data.cpp Source File

81 const int

PSL_COLUMN_COUNT(21);

86 auto

columnCount =

columns

.size();

87 if

(columnCount != PSL_COLUMN_COUNT && columnCount != PSL_COLUMN_COUNT+1) {

91 "PSL Error: Record has invalid column count."

);

126

vector<string> values;

129 for

(

const auto

value

: values) {

134 for

(

const auto

value

: values) {

139 for

(

const auto

value

: values) {

148 "PSL Error: Number of blockSizes does not match blockCount."

);

154 "PSL Error: Number of blockStartsQ does not match blockCount."

);

160 "PSL Error: Number of blockStartsT does not match blockCount."

);

174

ostr <<

"matches : "

mMatches

<<endl;

177

ostr <<

"nCount : "

mCountN

<<endl;

182

ostr <<

"strand : "

<< strand << endl;

183

ostr <<

"qName : "

<< nameQ << endl;

184

ostr <<

"qSize : "

mSizeQ

<< endl;

185

ostr <<

"qStart : "

mStartQ

<< endl;

186

ostr <<

"qEnd : "

mEndQ

<< endl;

187

ostr <<

"tName : "

<< nameT << endl;

188

ostr <<

"tSize : "

mSizeT

<< endl;

189

ostr <<

"tStart : "

mStartQ

<< endl;

190

ostr <<

"tEnd : "

mEndT

<< endl;

195 string

blockStartsQ =

197 string

blockStartsT =

200

ostr <<

"blockSizes : "

<< blockSizes << endl;

201

ostr <<

"blockStartsQ : "

<< blockStartsQ << endl;

202

ostr <<

"blockStartsT : "

<< blockStartsT << endl;

220 auto

& ids = denseSeg.

SetIds

();

221

ids.push_back(idResolver(

mNameQ

, 0,

true

));

222

ids.push_back(idResolver(

mNameT

, 0,

true

));

224

vector<SAlignSegment> segments;

226 for

(

const auto

& segment: segments) {

227

denseSeg.

SetLens

().push_back(segment.mLen);

228

denseSeg.

SetStarts

().push_back(segment.mStartQ);

229

denseSeg.

SetStarts

().push_back(segment.mStartT);

230

denseSeg.

SetStrands

().push_back(segment.mStrandQ);

231

denseSeg.

SetStrands

().push_back(segment.mStrandT);

233

denseSeg.

SetNumseg

(

static_cast<int>

(segments.size()));

238

pMatches->SetId().SetStr(

"num_match"

);

239

pMatches->SetValue().SetInt(

mMatches

);

240

denseSeg.

SetScores

().push_back(pMatches);

242

pMisMatches->SetId().SetStr(

"num_mismatch"

);

244

denseSeg.

SetScores

().push_back(pMisMatches);

246

pRepMatches->SetId().SetStr(

"num_repmatch"

);

248

denseSeg.

SetScores

().push_back(pRepMatches);

250

pCountN->SetId().SetStr(

"num_n"

);

251

pCountN->SetValue().SetInt(

mCountN

);

252

denseSeg.

SetScores

().push_back(pCountN);

258

vector<SAlignSegment>& segments)

const 262 if

(mBlockCount == 0) {

267

mBlockStartsQ[0], mBlockStartsT[0],

269 int

currentPosQ = mBlockStartsQ[0] + mBlockSizes[0];

270 int

currentPosT = mBlockStartsT[0] + mBlockSizes[0];

271 for

(

int i

=1;

< mBlockCount; ++

) {

272 auto

diffQ = mBlockStartsQ[

] - currentPosQ;

277 auto

diffT = mBlockStartsT[

] - currentPosT;

284

mBlockStartsQ[

], mBlockStartsT[

286

currentPosQ = mBlockStartsQ[

] + mBlockSizes[

];

287

currentPosT = mBlockStartsT[

] + mBlockSizes[

];

User-defined methods of the data storage class.

void xConvertBlocksToSegments(vector< SAlignSegment > &) const

void Initialize(const CPslReader::TReaderLine &)

CPslData(CReaderMessageHandler *=nullptr)

vector< int > mBlockStartsQ

void ExportToSeqAlign(CPslReader::SeqIdResolver, CSeq_align &seqAlign)

vector< int > mBlockStartsT

vector< int > mBlockSizes

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

static const column_t columns[]

@ eDiag_Error

Error message.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string JoinNumeric(TInputIterator from, TInputIterator to, const CTempString &delim)

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TScores & SetScores(void)

Assign a value to Scores data member.

void SetType(TType value)

Assign a value to Type data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

@ eType_partial

mapping pieces together

const GenericPointer< typename T::ValueType > T2 value

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