275 lines
6.8 KiB
C
275 lines
6.8 KiB
C
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/*
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Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
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All rights reserved.
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*/
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#include <xview/font.h>
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#include <xview/scrollbar.h>
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#include <xview/xview.h>
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#define TRUTH 1
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#define JUSTICE 2
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#define BEAUTY 3
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/*
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* Edit modes
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*/
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#define INSERT 0
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#define CHECK 1
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/*
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* Cursor directions
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*/
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#define RIGHT 1
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#define LEFT 0
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#define UP 0
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#define DOWN 1
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#ifndef TRUE
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#define TRUE 1
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#define FALSE 0
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#endif
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#define GBUFSIZ 512
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#define MAX_NA_DISPLAY_WIDTH 1024
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#define MAX_NA_DISPLAY_HEIGHT 1024
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#define MAX_STARTUP_CANVAS_HEIGHT 512
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#define grey_height 8
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#define grey_width 8
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/*
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* Definable dialog types
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*/
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#define TEXTFIELD 0x1
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#define SLIDER 0x2
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#define CHOOSER 0x3
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#define CHOICE_MENU 0x4
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#define CHOICE_LIST 0x5
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/*
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* File Formats
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*/
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#define GDE 0x100
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#define GENBANK 0x101
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#define NA_FLAT 0x102
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#define COLORMASK 0x103
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#define STATUS_FILE 0x104
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/*
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* Protection bits
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*/
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#define PROT_BASE_CHANGES 0x1 /* Allow base changes */
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#define PROT_GREY_SPACE 0x2 /* Allow greyspace modification */
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#define PROT_WHITE_SPACE 0x4 /* Allow whitespace modification */
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#define PROT_TRANSLATION 0x8 /* Allow translation */
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#define PROT_REORIENTATION 0x10 /* Allow reorientation */
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/*
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* File loading methods (must be 'OR/AND' able)
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*/
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#define NONE 0x0
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#define DESTROY 0x1
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#define LOAD 0x2
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#define SAVE 0x4
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#define SELECTED 0x8
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#define ALL 0x10
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#define SELECT_REGION 0x20
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#define SELECT_ONE 0x30
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/*
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* Sequence DISPLAY Types
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*/
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#define NASEQ_ALIGN 0x201
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#define NASEQ 0x202
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/*
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* Sequence Data Types
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*/
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#define DNA 0x300
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#define RNA 0x301
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#define TEXT 0x302
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#define MASK 0x303
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#define PROTEIN 0x304
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/*
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* extended sequence attributes (true/false)
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*/
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#define IS_5_TO_3 0x01 /* 5prime to 3 prime */
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#define IS_3_TO_5 0x02 /* 3 prime to 5 prime */
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#define IS_CIRCULAR 0x04 /* circular dna */
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#define IS_PRIMARY 0x10 /* on the primary strand */
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#define IS_SECONDARY 0x20 /* on the secondary strand */
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#define IS_MODIFIED 0x40 /* modification flag */
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#define IS_ORIG_PRIMARY 0x80 /* Original sequence was primary */
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#define IS_ORIG_SECONDARY 0x100 /* Original sequence was secondary */
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#define IS_ORIG_5_TO_3 0x200 /* Original sequence was 5_to_3 */
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#define IS_ORIG_3_TO_5 0x400 /* Original sequence was 3_to_5 */
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#ifdef HGL
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#define DEFAULT_X_ATTR 0
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#else
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#define DEFAULT_X_ATTR IS_5_TO_3+IS_PRIMARY;
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#endif
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/*
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* Other display attributed
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*/
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#define INVERTED 1
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#define VSCROLL_LOCK 2
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#define KEYCLICKS 4
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#define GDE_MESSAGE_PANEL 8
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/*
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* Coloring Methods
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*/
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#define COLOR_MONO 0x40 /* no color, simple black and white */
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#define COLOR_LOOKUP 0x41 /* Use a simple value->color lookup */
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#define COLOR_ALN_MASK 0x42 /* The alignment has a column by column color
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mask associated with it */
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#define COLOR_SEQ_MASK 0x43 /* Each sequence has a color mask*/
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#define COLOR_STRAND 0x44 /* Color based on original strandedness*/
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/*
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* Data types
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*/
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typedef struct
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{
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int *valu;
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} NumList;
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typedef struct
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{
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struct
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{
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int yy;
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int mm;
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int dd;
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int hr;
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int mn;
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int sc;
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} origin,modify;
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} TimeStamp;
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typedef unsigned char NA_Base;
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typedef struct
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{
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char *name;
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int type;
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NumList *list;
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int listlen;
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int maxlen;
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} GMask;
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typedef struct NA_SeqStruct
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{
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char id[80]; /* sequence id (ACCESSION)*/
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char seq_name[80]; /* Sequence name (ORGANISM) */
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char short_name[32]; /* Name (LOCUS) */
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char barcode[80];
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char contig[80];
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char membrane[80];
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char description[80]; /* Description (DEFINITION)*/
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char authority[80]; /* Author (or creator) */
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char *comments; /* Stuff we can't parse */
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int comments_len, comments_maxlen;
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NA_Base *sequence; /* List of bases */
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TimeStamp t_stamp; /* Time stamp of origin/modification */
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Mask *mask; /* List of masks(analysis/display) */
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int offset; /* offset into alignment (left white)
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space */
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int seqlen; /* Number of elements in sequence[] */
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int seqmaxlen; /* Size sequence[] (for mem alloc) */
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unsigned int protect; /* Protection mask */
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int attr; /* Extended attributes */
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int groupid; /* group id */
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int *col_lut; /* character to color LUT */
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struct NA_SeqStruct *groupb; /* Group link backward */
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struct NA_SeqStruct *groupf; /* Group link forward */
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int *cmask; /* color mask */
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int selected; /* Selection flag */
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int subselected; /* Sub selection flag */
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int format; /* default file format */
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int elementtype; /* what type of data are being aligned*/
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char *baggage; /* unformatted comments*/
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int baggage_len,
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baggage_maxlen;
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int *tmatrix; /* translation matrix (code->char) */
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int *rmatrix; /* reverse translation matrix
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(char->code)*/
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} NA_Sequence;
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typedef struct
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{
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char *id; /* Alignment ID */
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char *description; /* Description of the alignment*/
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char *authority; /* Who generated the alignment*/
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int *cmask; /* color mask */
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int cmask_offset; /* color mask offset */
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int cmask_len; /* color mask length */
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int ref; /* reference sequence */
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int numelements; /* number of data elements */
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int maxnumelements; /* maximum number of data elements */
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int nummasks; /* number of masks */
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int maxlen; /* Maximum length of alignment */
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int rel_offset; /* add this to every sequence offset */
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/* to orient it back to 0 */
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Mask *mask; /* masks */
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NA_Sequence *element; /* alignment elements */
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int numgroups; /* number of groups */
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NA_Sequence **group; /* link to array of pointers into
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each group */
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char *na_ddata; /* display data */
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int format; /* default file format */
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char *selection_mask; /* Sub sequence selection mask */
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int selection_mask_len; /* Sub selection mask length */
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int min_subselect; /* Leftmost coord of selection mask */
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} NA_Alignment;
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typedef struct
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{
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int font_dx; /* width of a character in this font*/
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int font_dy; /* height of a character in this font*/
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int wid,ht; /* width and height of edit win (in
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characters */
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int top_seq; /* Top sequence index shown */
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int lft_pos; /* Leftmost column (in alignment
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position coords) */
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int color_type; /* Method of manipulating colors
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(See above) */
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int depth; /* number of color bits available */
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int num_colors; /* Actual number of colors used */
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int *palette; /* palette for display */
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int *col_lut; /* character to color LUT */
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int black,white; /* color indicies for blk,wht */
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int cursor_x,cursor_y; /* Current cursor positions */
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int position; /* Current position minus whitespace */
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int *jumptbl; /* the jump table for fast access
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into the sequence data */
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int jtsize; /* its length */
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NA_Alignment *aln; /* Pointer to the actual data set
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(the alignment */
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Xv_font font; /* The default font */
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Canvas seq_can,nam_can; /* ties to the canvas for screen
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updates. */
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Window seq_x,nam_x; /* X versions of the above */
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int use_repeat; /* Number keys set repeat count*/
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} NA_DisplayData;
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#define getcmask(a,b) (b < ((a)->offset))?0:((a)->cmask[(b-(a)->offset)])
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#include "functions.h"
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