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// ================================================================ //
// //
// File : arbdb_base.h //
// Purpose : most minimal ARBDB interface //
// provide functions/types needed for arb_assert.h //
// //
// Coded by Ralf Westram (coder@reallysoft.de) in December 2008 //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// ================================================================ //
#ifndef ARBDB_BASE_H
#define ARBDB_BASE_H
#ifndef _GLIBCXX_CSTDIO
#include <cstdio>
#endif
#ifndef ARB_CORE_H
#include <arb_core.h>
#endif
#define NOT4PERL // function definitions starting with NOT4PERL are not included into the ARB-perl-interface
typedef const char *GB_CSTR; // read-only
typedef char *GB_BUFFER; // points to a piece of mem (writeable, but don't free!)*/
typedef const char *GB_CBUFFER; // points to a piece of mem (readable only)*/
struct GBDATA;
struct GB_HASH;
typedef int GBQUARK; // -1 = any quark, 0 = no quark, >0 explicit quark
typedef float GBT_LEN;
struct GBT_TREE;
typedef unsigned int GB_UINT4; // 4 byte! @@@ use uint32_t ?
typedef const unsigned int GB_CUINT4;
typedef unsigned long GB_ULONG;
typedef const float GB_CFLOAT;
enum GB_CB_TYPE {
GB_CB_NONE = 0,
GB_CB_DELETE = 1,
GB_CB_CHANGED = 2, // element or son of element changed
GB_CB_SON_CREATED = 4, // new son created
// convenience defs:
GB_CB_ALL = GB_CB_DELETE|GB_CB_CHANGED|GB_CB_SON_CREATED,
GB_CB_ALL_BUT_DELETE = GB_CB_ALL&~GB_CB_DELETE,
GB_CB_CHANGED_OR_DELETED = GB_CB_CHANGED|GB_CB_DELETE,
GB_CB_CHANGED_OR_SON_CREATED = GB_CB_CHANGED|GB_CB_SON_CREATED,
};
typedef void (*GB_CB)(GBDATA *, int *clientdata, GB_CB_TYPE gbtype);
enum GB_alignment_type {
GB_AT_UNKNOWN,
GB_AT_RNA, // Nucleotide sequence (U)
GB_AT_DNA, // Nucleotide sequence (T)
GB_AT_AA, // AminoAcid
};
enum NewickFormat { // bit-values
nSIMPLE = 0,
nLENGTH = 1,
nGROUP = 2,
nREMARK = 4,
nALL = nLENGTH|nGROUP|nREMARK,
};
#else
#error arbdb_base.h included twice
#endif // ARBDB_BASE_H
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