4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
7 * This class contains the sequence information. It should also contain
8 * the sequence name, and the encoded version.
9 * A vector of Sequences is passed to the Alignment object to set it up.
11 * Mark 22-1-2007: Added a unique sequence identifier to help with correct output
20 #include "../general/userparams.h"
21 #include "../general/utils.h"
30 Sequence(std::string& seq, std::string& name, std::string& title);
31 Sequence(std::string& seq, std::string& name, std::string& title,
33 Sequence(std::vector<int>* encodedSequence, std::string& name, std::string& title,
35 void encodeSequence();
37 std::vector<int>* getSequence();
39 std::string getName();
40 std::string getTitle();
42 unsigned long getIdentifier(){return identifier;}
47 void checkIntegrity();
48 void copyStringIntoVector(std::vector<char>* _vectorTo, std::string* _stringFrom);
51 std::vector<char> _sequence;
52 std::vector<int> _encodedSequence;
55 unsigned long identifier;