| 1 | // ================================================================ // |
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| 2 | // // |
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| 3 | // File : arbdb_base.h // |
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| 4 | // Purpose : most minimal ARBDB interface // |
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| 5 | // provide functions/types needed for arb_assert.h // |
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| 6 | // // |
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| 7 | // Coded by Ralf Westram (coder@reallysoft.de) in December 2008 // |
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| 8 | // Institute of Microbiology (Technical University Munich) // |
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| 9 | // http://www.arb-home.de/ // |
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| 10 | // // |
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| 11 | // ================================================================ // |
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| 12 | |
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| 13 | #ifndef ARBDB_BASE_H |
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| 14 | #define ARBDB_BASE_H |
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| 15 | |
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| 16 | #ifndef _GLIBCXX_CSTDIO |
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| 17 | #include <cstdio> |
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| 18 | #endif |
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| 19 | #ifndef ARB_CORE_H |
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| 20 | #include <arb_core.h> |
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| 21 | #endif |
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| 22 | |
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| 23 | #define NOT4PERL // function definitions starting with NOT4PERL are not included into the ARB-perl-interface |
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| 24 | |
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| 25 | typedef const char *GB_CSTR; // read-only |
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| 26 | typedef char *GB_BUFFER; // points to a piece of mem (writeable, but don't free!)*/ |
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| 27 | typedef const char *GB_CBUFFER; // points to a piece of mem (readable only)*/ |
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| 28 | |
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| 29 | struct GBDATA; |
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| 30 | struct GB_HASH; |
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| 31 | |
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| 32 | typedef int GBQUARK; // -1 = any quark, 0 = no quark, >0 explicit quark |
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| 33 | |
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| 34 | typedef float GBT_LEN; |
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| 35 | |
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| 36 | class TreeNode; |
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| 37 | class TreeRoot; |
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| 38 | |
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| 39 | typedef unsigned int GB_UINT4; // 4 byte! @@@ use uint32_t ? |
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| 40 | typedef const unsigned int GB_CUINT4; |
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| 41 | |
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| 42 | typedef unsigned long GB_ULONG; |
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| 43 | typedef const float GB_CFLOAT; |
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| 44 | |
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| 45 | |
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| 46 | enum GB_CB_TYPE { |
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| 47 | GB_CB_NONE = 0, |
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| 48 | GB_CB_DELETE = 1, |
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| 49 | GB_CB_CHANGED = 2, // element or son of element changed |
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| 50 | GB_CB_SON_CREATED = 4, // new son created |
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| 51 | |
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| 52 | // convenience defs: |
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| 53 | GB_CB_ALL = GB_CB_DELETE|GB_CB_CHANGED|GB_CB_SON_CREATED, |
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| 54 | GB_CB_ALL_BUT_DELETE = GB_CB_ALL&~GB_CB_DELETE, |
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| 55 | GB_CB_CHANGED_OR_DELETED = GB_CB_CHANGED|GB_CB_DELETE, |
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| 56 | GB_CB_CHANGED_OR_SON_CREATED = GB_CB_CHANGED|GB_CB_SON_CREATED, |
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| 57 | }; |
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| 58 | |
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| 59 | typedef void (*GB_CB)(GBDATA *, int *clientdata, GB_CB_TYPE gbtype); |
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| 60 | |
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| 61 | enum GB_alignment_type { |
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| 62 | GB_AT_UNKNOWN, |
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| 63 | GB_AT_RNA, // Nucleotide sequence (U) |
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| 64 | GB_AT_DNA, // Nucleotide sequence (T) |
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| 65 | GB_AT_AA, // AminoAcid |
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| 66 | }; |
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| 67 | |
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| 68 | enum NewickFormat { // bit-values |
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| 69 | nSIMPLE = 0, |
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| 70 | nLENGTH = 1, |
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| 71 | nGROUP = 2, |
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| 72 | nREMARK = 4, |
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| 73 | nWRAP = 8, |
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| 74 | |
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| 75 | nALL = nLENGTH|nGROUP|nREMARK, |
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| 76 | }; |
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| 77 | |
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| 78 | |
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| 79 | #else |
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| 80 | #error arbdb_base.h included twice |
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| 81 | #endif // ARBDB_BASE_H |
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