98 bool FastaReader::isChaste(const string& s, const string& line)  in isChaste()  argument
106 			"and saw `" << s << "' near\n" << line << endl;  in isChaste()
124 	assert(!seq.empty());  in isColourSpace()
190 			string line;  in read()  local
192 					&& getline(line))  in read()
193 				s += line;  in read()
201 				string line;  in read()  local
202 				getline(line);  in read()
208 					<< c << line << "\n";  in read()
216 		if (s.empty()) {  in read()
229 			s.erase(0, 2);  in read()
230 			q.erase(0, 1);  in read()
233 		if (!q.empty())  in read()
245 			s.erase(trimBack);  in read()
246 			s.erase(0, trimFront);  in read()
247 			if (!q.empty()) {  in read()
248 				q.erase(trimBack);  in read()
249 				q.erase(0, trimFront);  in read()
257 		string line;  in read()  local
260 		getline(line);  in read()
261 		istringstream in(line);  in read()
294 					<< line << endl;  in read()
321 			if (!q.empty())  in read()
327 					&& !isChaste(fields.back(), line)) {  in read()
335 				if (!fields[i].empty())  in read()
337 			if (!fields[6].empty() && fields[6] != "0")  in read()
344 			comment += isChaste(fields.back(), line)  in read()
354 					<< line << endl;  in read()
365 		s.erase(m_maxLength);  in read()
366 		q.erase(m_maxLength);  in read()
373 	if (opt::qualityThreshold > 0 && !q.empty()) {  in read()
382 			s.erase(1);  in read()
383 			q.erase(1);  in read()
385 			s.erase(trimBack);  in read()
386 			s.erase(0, trimFront);  in read()
387 			q.erase(trimBack);  in read()
388 			q.erase(0, trimFront);  in read()
392 	if (opt::internalQThreshold > 0 && !q.empty()) {  in read()