ARB
ed4_edit_string.hxx
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1 // =============================================================== //
2 // //
3 // File : ed4_edit_string.hxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef ED4_EDIT_STRING_HXX
12 #define ED4_EDIT_STRING_HXX
13 
14 #ifndef ED4_DEFS_HXX
15 #include "ed4_defs.hxx"
16 #endif
17 #ifndef CHARTABLE_H
18 #include <chartable.h>
19 #endif
20 
21 struct ED4_work_info;
22 
23 inline bool ED4_is_gap_character(char chr) { return BaseFrequencies::isGap(safeCharIndex(chr)); } // defined via user setting (ED4_AWAR_GAP_CHARS)
24 void ED4_setup_gaps_and_alitype(const char *gap_chars, GB_alignment_type alitype);
25 
26 const char SEQ_POINT = '.';
27 
28 class ED4_remap;
29 
30 class ED4_Edit_String : virtual Noncopyable {
31  GBDATA *gbd;
32  char *seq;
33  long seq_len;
34  ED4_remap *remap;
35  static int nrepeat;
36  static int nrepeat_is_already_set;
37  static int nrepeat_zero_requested;
38 
39  int legal_curpos(long pos) const { return pos>=0 && pos<=seq_len; }
40  int legal_seqpos(long pos) const { return pos>=0 && pos<seq_len; }
41 
42  GB_ERROR moveBase(long source_position, long dest_position, unsigned char gap_to_use); // moves a base from source_position to dest_position
43 
44  GB_ERROR shiftBases(long source_pos, long source_endpos, long dest_position,
45  int direction, long *dest_endpos, unsigned char gap_to_use); // shifts a line of bases from source_position to dest_position
46 
47  long get_next_base(long seq_position, int direction);
48  long get_next_gap(long seq_position, int direction);
49 
50  long get_next_visible_base(long position, int direction);
51  long get_next_visible_gap(long position, int direction);
52  long get_next_visible_pos(long position, int direction);
53 
54  GB_ERROR insert(char *, long position, int direction, int removeAtNextGap);
55  GB_ERROR remove(int len, long position, int direction, int insertAtNextGap);
56  GB_ERROR replace(char *text, long position, int direction);
57  GB_ERROR swap_gaps(long position, char ch);
58 
59  GB_ERROR command(AW_key_mod keymod, AW_key_code keycode, char key, int direction, ED4_EDITMODE mode, bool is_consensus,
60  long &cursorpos, bool& changed_flag, ED4_CursorJumpType& cursor_jump, bool& cannot_handle, bool& write_fault, GBDATA *gb_data, bool is_sequence);
61 
62  unsigned char get_gap_type(long pos, int direction);
63 
64 public:
65  char *old_seq;
67 
69  void init_edit();
71  void finish_edit();
73 
74  int use_nrepeat() { // external functions use this to get and use nrepeat
75  int nrep = nrepeat==0 ? 1 : nrepeat;
76  nrepeat = 0;
77  return nrep;
78  }
79 };
80 
81 #else
82 #error ed4_edit_string.hxx included twice
83 #endif // ED4_EDIT_STRING_HXX
ED4_EDITMODE
Definition: ed4_defs.hxx:30
CONSTEXPR_INLINE unsigned char safeCharIndex(char c)
Definition: dupstr.h:73
GB_ERROR edit(ED4_work_info *info) __ATTR__USERESULT
static bool isGap(char c)
Definition: chartable.h:248
GB_alignment_type
Definition: arbdb_base.h:61
ED4_CursorJumpType
Definition: ed4_defs.hxx:291
AW_key_code
Definition: aw_keysym.hxx:14
#define __ATTR__USERESULT
Definition: attributes.h:58
const char SEQ_POINT
bool ED4_is_gap_character(char chr)
AW_key_mod
Definition: aw_keysym.hxx:44
void ED4_setup_gaps_and_alitype(const char *gap_chars, GB_alignment_type alitype)
Definition: ED4_main.cxx:254
static int info[maxsites+1]