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Last change
on this file was
7272,
checked in by westram, 13 years ago
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merged from dev [7244] [7250] [7251] [7252] [7253] [7254] [7255] [7257] [7258] [7259] [7260] [7261] [7271]
- extracted conversion logic of absolute ↔ relative position into BasePosition
- refactored BI_ecoli_ref and ED4_base_position (using BasePosition)
- corrected input range of abs_2_rel ([0..N-1] → [0..N])
- clean up chaos caused by different semantics of positions (biological[1..N] vs informational[0..N-1])
- commented (hopefully) all AWARs and variables which use biological positions
- made semantic changes explicit by using bio2info() and info2bio()
- positions passed to/reported by PTserver are now biological positions. Affects
- probe design (absolute position, ecoli range restriction)
- probe match (absolute position, ecoli position (bugfix see below)).
- ProbeMatchParser does not change semantics
- fix several bugs
- ED4_jump_to_cursor_position limited position to screen before converting from relative to absolute position
- SEC_root::paintEcoliPositions added 1 to relative pos (instead of including position at cursor)
- ecoli position in probe match/PTserver (did not include ecoli-base at match position)
- ecoli range restriction in probe design/PTserver (check was broken, see [7261])
- base position for consensus terminals
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File size:
1.4 KB
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| 1 | // ================================================================= // |
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| 2 | // // |
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| 3 | // File : arb_defs.h // |
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| 4 | // Purpose : global defines and mini inlines // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in September 2010 // |
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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 ARB_DEFS_H |
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| 13 | #define ARB_DEFS_H |
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| 14 | |
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| 15 | #ifndef ARB_ASSERT_H |
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| 16 | #include <arb_assert.h> |
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| 17 | #endif |
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| 18 | |
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| 19 | #define ARRAY_ELEMS(array) (sizeof(array)/sizeof(array[0])) |
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| 20 | #define TERMINATED_ARRAY_ELEMS(array) (ARRAY_ELEMS(array)-1) |
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| 21 | |
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| 22 | // Internally ARB shall use position [0..N-1] for calculations. |
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| 23 | // Only while showing positions to the user, we use [1..N] (as well in displayed AWARs). |
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| 24 | // Please use the following functions to make the conversion explicit: |
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| 25 | |
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| 26 | inline int bio2info(int biopos) { arb_assert(biopos >= 1); return biopos-1; } |
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| 27 | inline int info2bio(int infopos) { arb_assert(infopos >= 0); return infopos+1; } |
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| 28 | |
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| 29 | |
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| 30 | #else |
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| 31 | #error arb_defs.h included twice |
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| 32 | #endif // ARB_DEFS_H |
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