| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : sec_abspos.hxx // |
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| 4 | // Purpose : Encapsulates helix position access // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in July 2007 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // =============================================================== // |
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| 11 | |
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| 12 | #ifndef SEC_ABSPOS_HXX |
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| 13 | #define SEC_ABSPOS_HXX |
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| 14 | |
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| 15 | #ifndef _CPP_CSTDIO |
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| 16 | #include <cstdio> |
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| 17 | #endif |
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| 18 | #ifndef ARBTOOLS_H |
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| 19 | #include <arbtools.h> |
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| 20 | #endif |
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| 21 | |
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| 22 | #ifndef SEC_DEFS_HXX |
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| 23 | #include "SEC_defs.hxx" |
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| 24 | #endif |
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| 25 | |
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| 26 | |
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| 27 | class XString : Noncopyable { |
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| 28 | char *x_string; |
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| 29 | size_t x_string_len; |
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| 30 | |
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| 31 | int x_count; // number of 'x's found in x_string |
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| 32 | |
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| 33 | size_t *abspos; // contains absolute positions for all 'x's in 'x_string' |
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| 34 | int *number_found; // for each absolute position P, contains number of 'x's from start of sequence till P-1 |
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| 35 | |
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| 36 | bool initialized; // true if initialize called |
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| 37 | |
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| 38 | void set_length(size_t len); // dealloc internal array if length grows |
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| 39 | |
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| 40 | void addX(size_t abs_pos) { // add an X at pos |
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| 41 | initialized = false; |
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| 42 | sec_assert(abs_pos<x_string_len); |
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| 43 | x_string[abs_pos] = 'x'; |
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| 44 | } |
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| 45 | |
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| 46 | public: |
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| 47 | XString(size_t ali_length); |
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| 48 | XString(const char *saved_x_string, size_t saved_len, size_t ali_length); |
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| 49 | ~XString(); |
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| 50 | |
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| 51 | void initialize(); // builds all internal data from x_string |
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| 52 | |
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| 53 | int getXcount() const { |
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| 54 | sec_assert(initialized); |
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| 55 | return x_count; |
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| 56 | } |
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| 57 | size_t getLength() const { return x_string_len; } |
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| 58 | |
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| 59 | size_t getAbsPos(int x) const; // gets absolute position of a 'x' |
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| 60 | int getXleftOf(size_t abspos) const; // gets the number of 'x's left of sequence pos |
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| 61 | |
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| 62 | void addXpair(size_t start, size_t end) { |
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| 63 | #if defined(DEBUG) && 0 |
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| 64 | printf("addXpair(%u, %u)\n", start, end); |
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| 65 | #endif // DEBUG |
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| 66 | addX(start); |
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| 67 | addX(end); |
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| 68 | } |
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| 69 | |
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| 70 | const char *get_x_string() const; // version saved to DB |
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| 71 | bool alignment_too_short() const { return x_string[x_string_len-1] == 'x'; } |
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| 72 | size_t get_x_string_length() const { return getLength() - (alignment_too_short() ? 0 : 1); } // version saved to DB |
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| 73 | }; |
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| 74 | |
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| 75 | #else |
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| 76 | #error sec_abspos.hxx included twice |
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| 77 | #endif // SEC_ABSPOS_HXX |
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