4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
12 #include "../alignment/Alignment.h"
13 #include "../alignment/Sequence.h"
14 #include "../general/userparams.h"
15 #include "../general/utils.h"
16 #include "FileParser.h"
17 #include "ClustalFileParser.h"
18 #include "PearsonFileParser.h"
19 #include "PIRFileParser.h"
20 #include "GDEFileParser.h"
21 #include "MSFFileParser.h"
22 #include "RSFFileParser.h"
23 #include "EMBLFileParser.h"
34 int seqInput(Alignment* alignPtr, bool append, string *offendingSeq);
35 int readSeqs(Alignment* alignPtr, int firstSeq, string *offendingSeq);
36 int profileInput(Alignment* alignPtr);
42 void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
44 string sequenceFileName;
45 bool noEmptySequence(vector<Sequence> seqRangeVector, string *offendingSeq);
50 vector<char> secStructMask; // Will need to be cleared out before every reading!
51 vector<char> gapPenaltyMask;
52 vector<string> formatNames;