| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : ed4_edit_string.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #ifndef ED4_EDIT_STRING_HXX |
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| 12 | #define ED4_EDIT_STRING_HXX |
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| 13 | |
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| 14 | #ifndef ED4_DEFS_HXX |
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| 15 | #include "ed4_defs.hxx" |
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| 16 | #endif |
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| 17 | #ifndef CHARTABLE_H |
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| 18 | #include <chartable.h> |
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| 19 | #endif |
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| 20 | |
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| 21 | struct ED4_work_info; |
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| 22 | |
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| 23 | inline bool ED4_is_gap_character(char chr) { return BaseFrequencies::isGap(safeCharIndex(chr)); } // defined via user setting (ED4_AWAR_GAP_CHARS) |
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| 24 | void ED4_setup_gaps_and_alitype(const char *gap_chars, GB_alignment_type alitype); |
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| 25 | |
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| 26 | const char SEQ_POINT = '.'; |
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| 27 | |
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| 28 | class ED4_remap; |
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| 29 | |
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| 30 | class ED4_Edit_String : virtual Noncopyable { |
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| 31 | GBDATA *gbd; |
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| 32 | char *seq; |
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| 33 | long seq_len; |
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| 34 | ED4_remap *remap; |
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| 35 | static int nrepeat; |
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| 36 | static int nrepeat_is_already_set; |
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| 37 | static int nrepeat_zero_requested; |
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| 38 | |
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| 39 | int legal_curpos(long pos) const { return pos>=0 && pos<=seq_len; } |
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| 40 | int legal_seqpos(long pos) const { return pos>=0 && pos<seq_len; } |
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| 41 | |
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| 42 | GB_ERROR moveBase(long source_position, long dest_position, unsigned char gap_to_use); // moves a base from source_position to dest_position |
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| 43 | |
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| 44 | GB_ERROR shiftBases(long source_pos, long source_endpos, long dest_position, |
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| 45 | int direction, long *dest_endpos, unsigned char gap_to_use); // shifts a line of bases from source_position to dest_position |
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| 46 | |
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| 47 | long get_next_base(long seq_position, int direction); |
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| 48 | long get_next_gap(long seq_position, int direction); |
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| 49 | |
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| 50 | long get_next_visible_base(long position, int direction); |
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| 51 | long get_next_visible_gap(long position, int direction); |
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| 52 | long get_next_visible_pos(long position, int direction); |
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| 53 | |
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| 54 | GB_ERROR insert(char *, long position, int direction, int removeAtNextGap); |
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| 55 | GB_ERROR remove(int len, long position, int direction, int insertAtNextGap); |
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| 56 | GB_ERROR replace(char *text, long position, int direction); |
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| 57 | GB_ERROR swap_gaps(long position, char ch); |
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| 58 | |
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| 59 | GB_ERROR command(AW_key_mod keymod, AW_key_code keycode, char key, int direction, ED4_EDITMODE mode, bool is_consensus, |
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| 60 | long &cursorpos, bool& changed_flag, ED4_CursorJumpType& cursor_jump, bool& cannot_handle, bool& write_fault, GBDATA *gb_data, bool is_sequence); |
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| 61 | |
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| 62 | unsigned char get_gap_type(long pos, int direction); |
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| 63 | |
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| 64 | public: |
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| 65 | char *old_seq; |
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| 66 | long old_seq_len; |
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| 67 | |
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| 68 | ED4_Edit_String(); |
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| 69 | void init_edit(); |
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| 70 | GB_ERROR edit(ED4_work_info *info) __ATTR__USERESULT; |
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| 71 | void finish_edit(); |
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| 72 | ~ED4_Edit_String(); |
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| 73 | |
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| 74 | int use_nrepeat() { // external functions use this to get and use nrepeat |
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| 75 | int nrep = nrepeat==0 ? 1 : nrepeat; |
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| 76 | nrepeat = 0; |
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| 77 | return nrep; |
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| 78 | } |
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| 79 | }; |
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| 80 | |
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| 81 | #else |
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| 82 | #error ed4_edit_string.hxx included twice |
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| 83 | #endif // ED4_EDIT_STRING_HXX |
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