| 1 | #ifndef Seq_h |
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| 2 | #define Seq_h |
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| 3 | |
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| 4 | #include <vector> |
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| 5 | |
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| 6 | class TextFile; |
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| 7 | class MSA; |
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| 8 | |
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| 9 | typedef std::vector<char> CharVect; |
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| 10 | |
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| 11 | class Seq : public CharVect |
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| 12 | { |
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| 13 | public: |
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| 14 | Seq() |
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| 15 | { |
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| 16 | m_ptrName = 0; |
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| 17 | // Start with moderate size to avoid |
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| 18 | // thrashing the heap. |
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| 19 | reserve(200); |
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| 20 | } |
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| 21 | virtual ~Seq() |
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| 22 | { |
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| 23 | delete[] m_ptrName; |
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| 24 | } |
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| 25 | |
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| 26 | private: |
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| 27 | // Not implemented; prevent use of copy c'tor and assignment. |
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| 28 | Seq(const Seq &); |
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| 29 | Seq &operator=(const Seq &); |
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| 30 | |
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| 31 | public: |
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| 32 | void Clear() |
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| 33 | { |
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| 34 | clear(); |
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| 35 | delete[] m_ptrName; |
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| 36 | m_ptrName = 0; |
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| 37 | m_uId = uInsane; |
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| 38 | } |
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| 39 | const char *GetName() const |
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| 40 | { |
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| 41 | return m_ptrName; |
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| 42 | } |
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| 43 | unsigned GetId() const |
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| 44 | { |
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| 45 | if (uInsane == m_uId) |
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| 46 | Quit("Seq::GetId, id not set"); |
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| 47 | return m_uId; |
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| 48 | } |
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| 49 | void SetId(unsigned uId) { m_uId = uId; } |
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| 50 | |
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| 51 | bool FromFASTAFile(TextFile &File); |
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| 52 | void ToFASTAFile(TextFile &File) const; |
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| 53 | void ExtractUngapped(MSA &msa) const; |
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| 54 | |
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| 55 | void FromString(const char *pstrSeq, const char *pstrName); |
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| 56 | void Copy(const Seq &rhs); |
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| 57 | void CopyReversed(const Seq &rhs); |
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| 58 | void StripGaps(); |
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| 59 | void StripGapsAndWhitespace(); |
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| 60 | void ToUpper(); |
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| 61 | void SetName(const char *ptrName); |
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| 62 | unsigned GetLetter(unsigned uIndex) const; |
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| 63 | unsigned Length() const { return (unsigned) size(); } |
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| 64 | bool Eq(const Seq &s) const; |
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| 65 | bool EqIgnoreCase(const Seq &s) const; |
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| 66 | bool EqIgnoreCaseAndGaps(const Seq &s) const; |
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| 67 | bool HasGap() const; |
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| 68 | unsigned GetUngappedLength() const; |
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| 69 | void LogMe() const; |
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| 70 | char GetChar(unsigned uIndex) const { return operator[](uIndex); } |
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| 71 | void SetChar(unsigned uIndex, char c) { operator[](uIndex) = c; } |
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| 72 | void AppendChar(char c) { push_back(c); } |
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| 73 | void FixAlpha(); |
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| 74 | |
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| 75 | #ifndef _WIN32 |
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| 76 | reference at(size_type i) { return operator[](i); } |
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| 77 | const_reference at(size_type i) const { return operator[](i); } |
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| 78 | #endif |
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| 79 | |
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| 80 | private: |
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| 81 | char *m_ptrName; |
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| 82 | unsigned m_uId; |
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| 83 | }; |
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| 84 | |
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| 85 | #endif // Seq.h |
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