GDE_def.h

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#ifndef GDE_DEF_H
#define GDE_DEF_H

#ifndef ARBDBT_H
#include <arbdbt.h>
#endif

/* Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
 * All rights reserved.
 */

#define gde_assert(bed) arb_assert(bed)

#define GBUFSIZ        4096
#define TEXTFIELDWIDTH 15

// Definable dialog types
#define TEXTFIELD      0x1
#define SLIDER         0x2
#define CHOOSER        0x3
#define CHOICE_MENU    0x4
#define CHOICE_LIST    0x5
#define CHOICE_TREE    0x6
#define CHOICE_SAI     0x7
#define CHOICE_WEIGHTS 0x8
#define FILE_SELECTOR  0x9

// File Formats
#define GDE         0x100
#define GENBANK     0x101
#define NA_FLAT     0x102

// File loading methods (must be 'OR/AND' able)
#define NONE          0x0
#define ALL           0x10

// Sequence DISPLAY Types
#define NASEQ_ALIGN 0x201

// Sequence Data Types
#define DNA     0x300
#define RNA     0x301
#define TEXT    0x302
#define MASK    0x303
#define PROTEIN 0x304

// extended sequence attributes (true/false)
#define IS_5_TO_3         0x01                      // 5prime to 3 prime
#define IS_3_TO_5         0x02                      // 3 prime to 5 prime
#define IS_CIRCULAR       0x04                      // circular dna
#define IS_PRIMARY        0x10                      // on the primary strand
#define IS_SECONDARY      0x20                      // on the secondary strand
#define IS_ORIG_PRIMARY   0x80                      // Original sequence was primary
#define IS_ORIG_SECONDARY 0x100                     // Original sequence was secondary
#define IS_ORIG_5_TO_3    0x200                     // Original sequence was 5_to_3
#define IS_ORIG_3_TO_5    0x400                     // Original sequence was 3_to_5

#define DEFAULT_X_ATTR  IS_5_TO_3+IS_PRIMARY;

// Data types

struct TimeStamp {
    struct {
        int yy;
        int mm;
        int dd;
        int hr;
        int mn;
        int sc;
    } origin, modify;
};

typedef unsigned char NA_Base;

// sizes for fields (including terminating zero byte)
#define SIZE_FIELD_GENBANK 80
#define SIZE_ID            SIZE_FIELD_GENBANK
#define SIZE_SEQ_NAME      SIZE_FIELD_GENBANK
#define SIZE_SHORT_NAME    32
#define SIZE_DESCRIPTION   SIZE_FIELD_GENBANK
#define SIZE_AUTHORITY     SIZE_FIELD_GENBANK

struct NA_Sequence {
    char  id[SIZE_ID];                  // sequence id (ACCESSION)
    char  seq_name[SIZE_SEQ_NAME];      // Sequence name (ORGANISM)
    char  short_name[SIZE_SHORT_NAME];  // Name (LOCUS)
    char  barcode[80];
    char  contig[80];
    char  membrane[80];
    char  description[SIZE_DESCRIPTION];// Description (DEFINITION)
    char  authority[SIZE_AUTHORITY];    // Author (or creator)
    char *comments;                     // Stuff we can't parse
    int   comments_len, comments_maxlen;

    NA_Base      *sequence;     // List of bases
    TimeStamp     t_stamp;      // Time stamp of origin/modification
    int           offset;       // offset into alignment (left white) space
    int           seqlen;       // Number of elements in sequence[]
    int           seqmaxlen;    // Size sequence[] (for mem alloc)
    int           attr;         // Extended attributes
    size_t        groupid;      // group id
    int          *col_lut;      // character to color LUT

    NA_Sequence *groupb;        // Group link backward
    NA_Sequence *groupf;        // Group link forward

    int   elementtype;          // what type of data are being aligned
    char *baggage;              // unformatted comments
    int   baggage_len, baggage_maxlen;
    int  *tmatrix;              // translation matrix (code->char)
    int  *rmatrix;              // reverse translation matrix (char->code)

    GBDATA  *gb_species;
};

struct NA_Alignment : virtual Noncopyable {
    char         *id;           // Alignment ID
    char         *description;  // Description of the alignment
    char         *authority;    // Who generated the alignment
    size_t        numelements;  // number of data elements
    int           maxnumelements; // maximum number of data elements
    int           maxlen;       // Maximum length of alignment
    int           rel_offset;   // add this to every sequence offset to orient it back to 0
    NA_Sequence  *element;      // alignment elements
    size_t        numgroups;    // number of groups
    NA_Sequence **group;        // link to array of pointers into each group
    int           format;       // default file format

    GBDATA            *gb_main;
    char              *alignment_name;
    GB_alignment_type  alignment_type;

    NA_Alignment(GBDATA *gb_main_);
    ~NA_Alignment();
};

inline void strcpy_truncate(char *dest, const char *source, size_t dest_size) { // @@@ move to arb_str.h?
    // like strncpy, but always writes terminating zero byte (truncating the result if necessary).
    // The number of copied non-zero-bytes does never exceed 'dest_size-1'.
    //
    // Behavior differing from standard strncpy:
    // - 'dest_size' is overall 'dest'-buffersize (incl. zero terminator)
    // - unused rest of dest buffer is not filled with 0 bytes

    arb_assert(dest_size>1);

    size_t copy_size = dest_size-1;
    size_t i         = 0;

    while (i<copy_size) {
        if (!source[i]) break;
        dest[i] = source[i];
        ++i;
    }

    arb_assert(i<dest_size);
    dest[i] = 0;
}

#else
#error GDE_def.h included twice
#endif // GDE_DEF_H