dna.h

unix或linux下的DNA分析软件源码 其功能如下 1. Edit up to 256 peptide or DNA sequences simultaneously. 2. Transla

                                 /* RESET = unmanage a dialog               */
    clickboxinfo *c[DCOUNT];     /* clickboxinfo struct needed in callbacks */             
                                       
                                 /* The following are needed in case dialog */
                                 /*    stays on the screen                  */
    Widget *widget;              /* Array of widgets to delete              */
    Widget form;                 /* Form widget to delete                   */
    int widgetcount;             /* no. of widgets on form                  */
    clickboxinfo *clickboxdata;  /* Array of clickboxinfo structs           */
                                 /* Function to call when button is clicked */
    void (*f1)(dialoginfo *a, int radio, int box, int boxbutton);   
    XtCBP radiocb[10];           /* Callback for RADIOPUSHBUTTONs           */
                                 /* Labels for RADIOPUSHBUTTONs             */
    char radiopushbuttonlabel[10][100];
    void *radiopushbuttonptr[10];/* Data to send to RADIOPUSHBUTTONs        */
    int list_editrow[DCOUNT];    /* Minimum list item that can be edited    */
    int list_editcol[DCOUNT];    /* Minimum column in list item one can edit*/
                                 /* Max column in list item                 */
    int list_maxstringsize[DCOUNT];

} Dialog;


typedef struct pushbuttoncbstruct
{  int button;
   Widget widget;
   char string[100];
   char command[100];
};


typedef struct ButtonStruct
{   int button;
    int state;
    Widget widget;
    char *label;
    char *activate_cmd;
    char *deactivate_cmd;
} buttonStruct;



typedef struct DOCUMENT
{   int          row, col;   // Cursor screen position
    int          pos;        // Cursor position from start of text
    int          text_direction;
    int          spacing;    // Spacing in pixels between lines - is large
                             //  because sequences are interleaved.
    int          touched;
    int          charwidth;
    int          charheight;
    int          topline;
    int          marked;
    int          markstart;
    int          markend;
    int          linestodisplay;
    int          n;          // No. of bases (i.e. text length)
    int          on;         // Original no. of bases (for undo)
    int          offset;     // Bases offset for alignment
    int          ncomments;  // No. of comments found in file
    int          type;       // PROTEIN or DNA
    int          otype;      // Original type, PROTEIN or DNA
    int          frame;      // Current reading frame (0-2)
    char        *text;       // Sequence in display format (DNA or Protein)
    char        *dtext;      // Current DNA form of sequence
                             // (MUST be kept in sync with 'text').
    char        *otext;      // original DNA or Protein text for undo
    char       **comment;    // Comments found in file
    char        *filename;
    XFontStruct *fontstruct;
} Document;


typedef struct Globals
{
    int     nbuttons;          // No. of user-defined buttons at left
    ButtonStruct **button;     // User-defined buttons at left
    Display  *display;         // Connection to X display  
    GC       gc;               // The graphics context for main
    uint     mask;
    Widget   main_widget;
    Widget   dialogdone;
    Widget   menu;
    Widget   menubar;
    Widget   helix_frame;
    Widget   draw_widget;
    Widget   drawing_area;
    Widget   button_drawing_area;
    Widget   match_area;
    Window   root_window;
    Window   main_window;
    Window   draw_window;
    Window   xlabel_window;
    Window   ylabel_window;
    Visual  *visual;
    Colormap colormap;
    XFontStruct  *fontstruct;  // Default font
    XmFontList    fontlist;    // Font list for Motif 1.2 and below
    int swap_temp;
    double   fswap_temp;       // Temporary double for swap macro
    double   dswap_temp;       // Temporary double for swap macro
    double   rr, cc;           // Column and row passed to expression evaluator
    char    *appname;          // Application's name
    char     homedir[FILENAMELENGTH];        // $HOME/.xdata directory for xdata.ini
    char     currentdir[FILENAMELENGTH];       // Current directory
    char     filename[FILENAMELENGTH];         // Filename
    char    *font;             // Name of font
    char    *macrotext;
    int      printer_device;
    char     printer_command[FILENAMELENGTH];  
    char     printer_name[FILENAMELENGTH]; 
    char     printer_file[FILENAMELENGTH]; 
    char     startdir[FILENAMELENGTH];         // Start-up directory
    char     version[100];
    char     nomemory[22];

    int      xres, yres;                 // Size of root window
    int      main_xsize;                 // Size of entire window
    int      main_ysize;
    int      main_xpos;
    int      main_ypos;
    int      xsize;                      // Size of drawing window for sequences
    int      ysize;                      
    int      mouse_button;
    int      bitsperpixel;
    uint     udepth;
    int      ximage_byte_order;
    int      sparse_packing;             // 1 = X windows sparse pseudo 24bpp mode
    int      sparse;                     // 1 = force 32 bpp instead of 24 bpp
    int      nosparse;                   // 1 = force 24 bpp instead of 32 bpp
    int      bcolor;
    int      hcolor;
    int      cols; 
    int      fcolor;
    int      getout;              // Flag for 'cancel'
    int      key_ascii;
    int      key_alt;
    int      key_ctrl;
    int      key_shift;
    int      rows;
    int      screen;
    int      signif;              // Significant digits to display
    int      state;               // Program button-pressing state
    int      want_messages;
    int      xlib_cursor;
    int      want_colormaps;
    int      main_fcolor, main_bcolor;
    int      graph_active;        // 1=files still open in graph fifo
    int      autoupdate;          // 1=automatically update graph when spreadsheet refreshed
    int      touched;             // 1=data has been changed
    int      editing;             // 0=correlation plot 1=editor
    int      off[64];
    Document *doc;
    uchar  **stringbufr;          // Image buffer for strings
    uchar  *stringbufr_1d;        // 1d alias for stringbufr
    XImage *stringbufr_ximage;    // XImage form of stringbufr for Xlib
    Pixmap spixmap;
    uchar  **image;               // Image buffer for plotting sequence data
    uchar  *image_1d;             // 1d alias for image
    XImage *image_ximage;         // XImage form of image  for Xlib
    int sequence_mode;
    int editmode;                 // 0=protein 1=dna 
    int noofsequences;            // No. of sequences being edited
    int cs;                       // Current sequence no.
    int alignsize;                // Sequence size to maximize matches for.
                                  //  (0 = use entire sequence) 
    int save_format;              // SCREEN or HIGHLIGHT
    int matrix_set1;
    int matrix_set2;
};

 
//--------------Function Prototypes------------------//


Widget addlabel(Widget parent, char *string, int position, double x1, double y1, 
   double x2, double y2);
Widget add_mainbutton(char *name, void *cb);
Widget openwindow(listinfo *l, Widget *listwidget, Widget *w, int *count);
XImage *createximage(int xsize, int ysize, int bpp, uchar *buf_1d);
Pixmap createpixmap(int x, int y, Window win);
uint **make_2d_alias(uint *b, int x, int y);
uchar **make_2d_alias(uchar *b, int x, int y);
double align(void);
double alignment(char *s1, char *s2, int offset);
double **make_2d_alias(double *b, int x, int y);
double clickbox(char* title, double fstartval, double fminval, double fmaxval, void f(double answer), int helptopic);
double molecular_weight(int cs);
double peptide_frequency(int cs);
char *basefilename(char* pathname);
char *gcvt(double val, int signif, char *buf);
char *getfilename(char *oldtitle);
char **getfilenames(int *count);
char *itoa(int value, char *str, int radix);
char *ltoa(long int value, char *str, int radix);
char *strupr(char *s);
char *strlwr(char *s);

uint pixelat(uchar* p, int bpp);
int between(int a,int b,int c);
int between(double a, double b, double c);
int bits_per_pixel(void);
int cant_overwrite_file(char* filename);
int clickbox(char* title, int startval, int minval, int maxval, void f(int answer), int helptopic);
int clickbox(char* title, int startval, int minval, int maxval, void f1(int answer), void f2(double answer), int decimalpoints, int type, int helptopic);
int dna2protein(char *code);
int drawmarkedline(int x, int y, char *s, int ms, int me, int w, int cw);
int execute(char *command, int noofargs, char **arg);
int filesize(char *filename);
int handle_keypress(KeySym keysym, char *keystring);
int **make_2d_alias(int *b, int x, int y);
int matchable_base(int c, int mode);
int message(char *heading);
int message(char *heading, int mode);
int message(char *heading, char *returnstring, int mode, int maxstringsize);
int multiclickbox(char* title, int noofboxes, clickboxinfo* a, void f(int values[10]), int helptopic);
int redrawscreen(int xx1, int yy1, int xx2, int yy2);
int save_ok(int ino);
int stringtohex(char* string);
int totalspacing(void);
int valid_base(int c, int mode);

void abouttheprogram(void);
void additemtolist(Widget w, Widget form, char *s, int showpos);
void addstandardbuttons(Widget form, Widget buttons[3], int *data); 
void addOkCancelHelpButtons(Widget form, Widget button[3], char *s1, int x1, 
   char *s2, int x2, char *s3, int x3, int *data);
void analyze(void);
void close(void);
void closewindow(Widget form, Widget *widgetlist, int wc);
void comments(void);
void configure(void);
void compare(void);
void compare(char *s1, char *s2, int n1, int n2, uchar **image);
void copyimage(int x1, int y1, int x2, int y2, int xoff, int yoff,
                int mode, XImage *ximage, Window win);
void count_bases(int cs, int *count, int &n);
void create_main_icon(void);
void down(void);
void dialogbox(dialoginfo &a);
void edit(void);
void error_message(char *s, int error);
void event_loop(Widget w);
void get_next_word(char *buffer, char *word, int maxlen, int &start);
void help(int helptopic);
void initialize_data(void);
void initialize_globals(void);
void init_editor(int k);
void init_xlib(void);
void left(void);
void list(listinfo *l); 
void makewidgets(Widget parent);
void move_cursor(int k, int lineno, int pos);
void nextframe(void);
void null(int a);
void null(int a[10]);
void null(double a);
void null(void);
void null(dialoginfo *a, int b, int c, int d);
void parsecommand(char *cmd, char **arg, int &noofargs, int maxlen, int maxargs);
void path(char *pathname, char *path);
void prevframe(void);
void print(char *string,int x, int y, uint fcol, uint bcol, Window win, 
      int wantbkg, int vertical);
void printcheck(dialoginfo *a, int radio, int box, int boxbutton);
void printmatches(int matches, int mismatches);
void printsequence(void);
void printstatus(int state);
void push_main_button(int k);
void putpixelbytes(uchar *address, int color, int depth);
void readsequence(void);
void readsettings(void);
void remove_trailing_junk(char *s);
void reset_user_buttons(void);
void resize_draw_widget(int xsize, int ysize);
void resize_main_widget(int xsize, int ysize);
void reverse(void);
void right(void);
void save(int needfilename=1);
void save_screen_image(FILE *fp);
void save_screen_text(FILE *fp);
void savesettings(void);
void search(char *searchstring);
void select(void);
void set_offset(int cs);
void set_sequence_mode(int mode);
void statistics(void);
void toggle_sequence_mode(void);
void text_size(char *s, int &xsize, int &ysize, int &ascent, int &descent);
void translate(int wantcheck);
void undo(void);
void unpush_main_button(int k);
void unpush_null_buttons(void);
void up(void);
void xminitializemisc(Widget parent);

//----------------------Callbacks----------------------//

void armboxcb(Widget w, XtP client_data, XmACB *call_data);
void cancelcb(Widget w, XtPointer client_data, XmACB *call_data);
void cancelmsgcb(Widget w, XtPointer client_data, XmACB *call_data);
void clickboxcb(Widget w, XtPointer client_data, XmACB *call_data);
void configurecb(Widget w, XtP client_data, XEvent *event);
void dialogclickboxcb(Widget w, XtP client_data, XmACB *call_data);
void dialogcursorcb(Widget w, XtP client_data, XmACB *call_data);
void dialogdoubleclickboxcb(Widget w, XtPointer client_data, XmACB *call_data);
void dialogfilenamecb(Widget w, XtP client_data, XmACB *call_data);
void dialoglistcb(Widget w, XtP client_data, XmACB *call_data);
void dialogmulticlickboxcb(Widget w, XtPointer client_data, XmACB *call_data);
void dialogstringcb(Widget w, XtP client_data, XmACB *call_data);
void drawcb(Widget widget, XtP client_data, XtP *call_data);
void drawinputcb(Widget widget, XtP client_data, XtP *call_data);
void entercb(Widget w, XtPointer client_data, XEvent *event);
void disarmcb(Widget w, XtPointer client_data, XmACB *call_data);
void executecb(Widget w, XtPointer client_data, XmACB *call_data);
void filenamecb(Widget widget, XtPointer client_data, XmACB *call_data);
void focuscb(Widget w, XtP client_data, XEvent *event);
void fscancelcb(Widget w, XtPointer client_data, XmFSBCB *call_data);
void fscdcb(Widget w, XtPointer client_data, XmFSBCB *call_data);
void fsokcb(Widget w, XtPointer client_data, XmFSBCB *call_data);
void fsseqnocb(Widget w, XtPointer client_data, XmFSBCB *call_data);
void helixcb(Widget widget, XtP client_data, XtP *call_data);
void helpcb(Widget w, XtPointer client_data, XmACB *call_data);
void listcb(Widget w, XtPointer client_data, XmACB *call_data);
void mainbuttoncb(Widget w, XtPointer client_data, XmACB *call_data);
void maincancelcb(Widget w, XtPointer client_data, XmACB *call_data);
void nomsgcb(Widget w, XtPointer client_data, XmACB *call_data);
void okcb(Widget w, XtPointer client_data, XmACB *call_data);
void okmsgcb(Widget w, XtPointer client_data, XmACB *call_data);
void promptmsgcb(Widget w, XtPointer client_data, XmACB *call_data);
void quitcb(Widget w, XtPointer client_data, XmACB *call_data);
void raisecb(Widget w, XtP client_data, XEvent *event);
void savecb(Widget w, XtPointer client_data, XmACB *call_data);
void slidercb(Widget w, XtPointer client_data, XmACB *call_data);
void timer_callback(XtPointer client_data, XtIntervalId *timer_id);
void toggleboxcb(Widget w, XtP client_data, XmACB *call_data);
void togglecb(Widget w, XtP client_data, XmACB *call_data);
void warningmessagecb(String aaa);