| 1 | #ifndef SeqVect_h |
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| 2 | #define SeqVect_h |
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| 3 | |
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| 4 | #include <vector> |
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| 5 | #include "seq.h" |
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| 6 | |
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| 7 | typedef std::vector<Seq *> SeqVectBase; |
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| 8 | |
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| 9 | class SeqVect : public SeqVectBase |
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| 10 | { |
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| 11 | public: |
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| 12 | SeqVect() {} |
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| 13 | virtual ~SeqVect(); |
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| 14 | |
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| 15 | private: |
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| 16 | // Not implemented; prevent use of copy c'tor and assignment. |
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| 17 | SeqVect(const SeqVect &); |
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| 18 | SeqVect &operator=(const SeqVect &); |
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| 19 | |
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| 20 | public: |
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| 21 | void FromFile(TextFile &File) |
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| 22 | { |
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| 23 | FromFASTAFile(File); |
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| 24 | } |
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| 25 | |
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| 26 | void FromFASTAFile(TextFile &File); |
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| 27 | void ToFASTAFile(TextFile &File) const; |
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| 28 | |
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| 29 | void ToFile(TextFile &File) const |
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| 30 | { |
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| 31 | ToFASTAFile(File); |
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| 32 | } |
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| 33 | |
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| 34 | void PadToMSA(MSA &msa); |
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| 35 | void Copy(const SeqVect &rhs); |
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| 36 | void StripGaps(); |
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| 37 | void StripGapsAndWhitespace(); |
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| 38 | void ToUpper(); |
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| 39 | void Clear(); |
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| 40 | unsigned Length() const { return (unsigned) size(); } |
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| 41 | unsigned GetSeqCount() const { return (unsigned) size(); } |
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| 42 | void AppendSeq(const Seq &s); |
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| 43 | bool FindName(const char *ptrName, unsigned *ptruIndex) const; |
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| 44 | void LogMe() const; |
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| 45 | const char *GetSeqName(unsigned uSeqIndex) const; |
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| 46 | unsigned GetSeqId(unsigned uSeqIndex) const; |
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| 47 | unsigned GetSeqIdFromName(const char *Name) const; |
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| 48 | unsigned GetSeqLength(unsigned uSeqIndex) const; |
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| 49 | void SetSeqId(unsigned uSeqIndex, unsigned uId); |
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| 50 | Seq &GetSeq(unsigned uIndex); |
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| 51 | Seq &GetSeqById(unsigned uId); |
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| 52 | const Seq &GetSeq(unsigned uIndex) const; |
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| 53 | |
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| 54 | ALPHA GuessAlpha() const; |
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| 55 | void FixAlpha(); |
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| 56 | |
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| 57 | #ifndef _WIN32 |
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| 58 | reference at(size_type i) { return operator[](i); } |
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| 59 | const_reference at(size_type i) const { return operator[](i); } |
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| 60 | #endif |
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| 61 | }; |
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| 62 | |
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| 63 | #endif // SeqVect_h |
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