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);

126

alignments.push_back(alignment);

141 ERRORMSG

(

"SequenceViewer::ReplaceAlignment() - bad parameters"

);

147

alignments.push_back(newAln);

167

SequenceList::const_iterator s, se = sequenceList->end();

168 for

(s=sequenceList->begin(); s!=se; ++s) {

171 if

(!(*s)->parentSet->IsMultiStructure() &&

172

(*s)->parentSet->objects.front()->mmdbID != (*s)->identifier->mmdbID)

continue

;

194 const

vector < int >& rowOrder,

198 unsigned int

firstCol = 0, lastCol = alignment->

() - 1, nColumns = 70;

199 if

(lastCol >= alignment->

() || firstCol > lastCol || nColumns < 1) {

200 ERRORMSG

(

"DumpFASTA() - nonsensical display region parameters"

);

208 bool

anyRepeat =

false

;

212

list < string >& titleList = idMap[seq->

identifier

];

216 if (titleList.size() == 0) { 218 // create full title line for first instance of this sequence 219 CBioseq::TId::const_iterator i, ie = seq->bioseqASN->GetId().end(); 220 for (i=seq->bioseqASN->GetId().begin(); i!=ie; ++i) { 221 if (i != seq->bioseqASN->GetId().begin()) 223 oss << (*i)->AsFastaString(); 225 string descr = seq->GetDescription(); 226 if (descr.size() > 0) 231 oss << "lcl|instance #" << (titleList.size() + 1) << " of " << seq->identifier->ToString(); 236 titleList.resize(titleList.size() + 1); 237 titleList.back() = (string) CNcbiOstrstreamToString(oss); 240 static const int eAllRepeats=0, eFakeRepeatIDs=1, eNoRepeats=2; 241 int choice = eAllRepeats; 244 wxArrayString choices; 245 choices.Add("Include all repeats with normal IDs"); 246 choices.Add("Include all repeats, but use unique IDs"); 247 choices.Add("Include no repeated sequences"); 248 choice = wxGetSingleChoiceIndex("How do you want to handle repeated sequences?", 249 "Choose repeat type", choices); 250 if (choice < 0) return; // cancelled 253 // output each alignment row (in order of the display) 254 unsigned int paragraphStart, nParags = 0, i; 256 Vector color, bgColor; 257 bool highlighted, drawBG; 258 for (row=0; row<alignment->NRows(); ++row) { 259 const Sequence *seq = alignment->GetSequenceOfRow(rowOrder[row]); 262 list < string >& titleList = idMap[seq->identifier]; 263 if (choice == eAllRepeats) { 264 os << titleList.front(); // use full id 265 } else if (choice == eFakeRepeatIDs) { 266 os << titleList.front(); 267 titleList.pop_front(); // move to next (fake) id 268 } else if (choice == eNoRepeats) { 269 if (titleList.size() > 0) { 270 os << titleList.front(); 271 titleList.clear(); // remove all ids after first instance 277 // split alignment up into "paragraphs", each with nColumns 278 for (paragraphStart=0; (firstCol+paragraphStart)<=lastCol; paragraphStart+=nColumns, ++nParags) { 279 for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) { 280 if (alignment->GetCharacterTraitsAt(firstCol+paragraphStart+i, rowOrder[row], justification, 281 &ch, &color, &highlighted, &drawBG, &bgColor)) { 283 os << (isA2M ? '

' : '

'); 285 os << (isA2M ? ch : (char) toupper((unsigned char) ch)); 287 ERRORMSG("GetCharacterTraitsAt failed!"); 294 static string ShortAndEscapedString(const string& s) 297 for (unsigned int i=0; i<s.size(); ++i) { 308 const

vector < int >& rowOrder,

312 #define LEFT_JUSTIFY resetiosflags(IOS_BASE::right) << setiosflags(IOS_BASE::left) 313 #define RIGHT_JUSTIFY resetiosflags(IOS_BASE::left) << setiosflags(IOS_BASE::right) 316 unsigned int

firstCol = 0, lastCol = alignment->

() - 1, nColumns = 60;

318 if

(lastCol >= alignment->

() || firstCol > lastCol || nColumns < 1) {

319 ERRORMSG

(

"DumpText() - nonsensical display region parameters"

);

328

vector < string > titles(alignment->

()), uids(doHTML ? alignment->

() : 0);

329 unsigned int

alnRow,

, maxTitleLength = 0, maxSeqLocStrLength = 0, leftMargin, decimalLength;

330 for

(alnRow=0; alnRow<alignment->

(); ++alnRow) {

331 row

= rowOrder[alnRow];

335 if

(titles[

size

() > maxTitleLength) maxTitleLength = titles[

].size();

336

decimalLength = ((

int

)

log10

((

double

) sequence->

Length

())) + 1;

337 if

(decimalLength > maxSeqLocStrLength) maxSeqLocStrLength = decimalLength;

356

leftMargin = maxTitleLength + maxSeqLocStrLength + 2;

360

vector < int > lastShownSeqLocs(alignment->

());

361 unsigned int

alnLoc,

;

364 bool

highlighted, drawBG;

365 for

(alnRow=0; alnRow<alignment->

(); ++alnRow) {

366 row

= rowOrder[alnRow];

367

lastShownSeqLocs[

] = -1;

368 for

(alnLoc=0; alnLoc<firstCol; ++alnLoc) {

370

&ch, &

color

, &highlighted, &drawBG, &bgCol))

372 if

(ch !=

'~'

) lastShownSeqLocs[