static void plotBP(char* sequence, short* structure)
{
int i;
int length;
float lx, ly;
float arcx, arcy, rad;
length = (int)strlen(sequence) ;
setlinestyle(SOLID);
setcolor(BLACK);
for(i = 0; i<length; i++) {
if(structure[i] > i) {
lx = structure[i] - i + 1;
//drawline((i+0.5)*CELLSIZE, length*CELLSIZE/2 - 1, (i + 0.5)*CELLSIZE, (length+lx)*CELLSIZE/2 -1);
flushinput();
//drawline((structure[i]-0.5)*CELLSIZE, length*CELLSIZE/2-1,(structure[i]-0.5)*CELLSIZE, (length+lx)*CELLSIZE/2 -1);
flushinput();
//drawline((i+0.5)*CELLSIZE, (length+lx)*CELLSIZE/2-1, (structure[i]-0.5)*CELLSIZE, (length+lx)*CELLSIZE/2-1);
arcx = (i + structure[i] )/2.0 * CELLSIZE;
arcy = length*CELLSIZE/2 -1;
rad = (structure[i] - 1 - i )/2.0 *CELLSIZE;
drawarc(arcx, arcy, rad, 0, -180.0);
flushinput();
}
}
}
void PlotRna(char* seqName, char* sequence, short* structure, char* filename, float score)
{
/*A:red, U: Green, G:Blue, C:Yellow*/
int i, j;
int length;
int sizex, sizey;
fname = filename;
length = (int)strlen(sequence) ;
sizex = length;
sizey = length;
/*printf("here......length %d\n",length);*/
drawInit(length, length, seqName, filename, score);
/* print out stems */
int st, stp;
char* c = (char*)malloc(sizeof(char)*1000);
i = 0; j = 0;
while(i < length) {
while(i < length && (structure[i] == 0 || structure[i] < i)) i++;
st = i;
while(i < length && (structure[i]-1 == structure[i+1])) i++;
stp = i;
if (i >= length) break;
sprintf(c, "%d-%d; %d-%d ",st+1, stp+1, structure[stp],structure[st]);
i++; j++;
if ((j%2) == 1) drawtext (sizex*CELLSIZE/4,sizey*CELLSIZE/10.0+((int)(j/2)+1)*CELLSIZE*sizey/30,c,1.0e6);
else drawtext (sizex*CELLSIZE/2,sizey*CELLSIZE/10.0+((int)(j/2))*CELLSIZE*sizey/30,c,1.0e6);
flushinput();
}
for(i=0; i<length; i++) {
if(sequence[i] == 'A' || sequence[i] == 'a')
setcolor(RED);
else if(sequence[i] == 'U'|| sequence[i] == 'u' || sequence[i] == 'T' || sequence[i] == 't')
setcolor(GREEN);
else if(sequence[i] == 'G' || sequence[i] == 'g')
setcolor(BLUE);
else if(sequence[i] == 'C' || sequence[i] == 'c')
setcolor(YELLOW);
else
setcolor(BLACK);
fillrect((i+0.2)*CELLSIZE, (sizey/2 - 0.8)*CELLSIZE, (i+0.8)*CELLSIZE, (sizey/2 - 0.2)*CELLSIZE);
flushinput();
}
plotBP(sequence, structure);
close_postscript();
close_graphics();
}
static void drawInit( int sizex, int sizey, char* seqName, char* filename, float score) {
int i,k=0;
int x,y;
char* c;
c =(char*)malloc(sizeof(char)*1000);
/* initialize display */
init_graphics("RNA");
/* still picture drawing allows user to zoom, etc. */
init_world (0.,0.,CELLSIZE*sizex,CELLSIZE*sizey);
//event_loop(button_press, drawscreen);
/* animation section */
clearscreen();
init_postscript(filename);
clearscreen();
sprintf(c, "%s%s%s%d%s%f%s", "RNA: ", seqName, ", length = ", sizex, ", energy = ",-score/1000.0, " kal/mol");
//printf(" output string is %s\n",c);
update_message("RNA secondary structure");
flushinput();
drawtext (sizex*CELLSIZE/2,sizey*CELLSIZE/10,c,1.0e6);
flushinput();
setcolor (BLACK);
setlinewidth(1);
setlinestyle (SOLID);
for (i=0;i<=sizex;i++) {
drawline (i*CELLSIZE,(sizey/2-1)*CELLSIZE,i*CELLSIZE,CELLSIZE*sizey/2);
flushinput();
}
drawline(0,(sizey/2-1)*CELLSIZE, sizex*CELLSIZE, CELLSIZE*(sizey/2-1));
drawline(0,sizey*CELLSIZE/2, sizex*CELLSIZE, CELLSIZE*sizey/2);
flushinput();
free(c);
}
void update_screen (int priority, char *msg, enum pic_type
pic_on_screen_val, boolean crit_path_button_enabled) {
/* Updates the screen if the user has requested graphics. The priority *
* value controls whether or not the Proceed button must be clicked to *
* continue. Saves the pic_on_screen_val to allow pan and zoom redraws. */
if (!show_graphics) /* Graphics turned off */
return;
/* If it's the type of picture displayed has changed, set up the proper *
* buttons. */
if (pic_on_screen != pic_on_screen_val) {
if (pic_on_screen_val == PLACEMENT && pic_on_screen == NO_PICTURE) {
create_button ("Window", "Toggle Nets", toggle_nets);
}
else if (pic_on_screen_val == ROUTING && pic_on_screen == PLACEMENT) {
create_button ("Toggle Nets", "Toggle RR", toggle_rr);
create_button ("Toggle RR", "Congestion", toggle_congestion);
if (crit_path_button_enabled)
create_button ("Congestion", "Crit. Path", highlight_crit_path);
}
else if (pic_on_screen_val == PLACEMENT && pic_on_screen == ROUTING) {
destroy_button ("Toggle RR");
destroy_button ("Congestion");
if (crit_path_button_enabled)
destroy_button ("Crit. Path");
}
}
/* Save the main message. */
strncpy (default_message, msg, BUFSIZE);
pic_on_screen = pic_on_screen_val;
update_message (msg);
drawscreen();
if (priority >= gr_automode) {
event_loop(highlight_blocks, drawscreen);
}
else {
flushinput();
}
}
char *xmodemTransmit(int fnbr)
{
unsigned char xbuff[X_BUF_SIZE];
unsigned char packetno = 1;
int i, c, len = 0;
int retry;
// first establish communication with the remote
while(1) {
for( retry = 0; retry < 16; ++retry) {
if ((c = _inbyte((DLY_1S)<<1)) >= 0) {
switch (c) {
case NAK: // start sending
goto start_trans;
case CAN:
if ((c = _inbyte(DLY_1S)) == CAN) {
MMputchar(ACK);
flushinput();
return "Cancelled by remote";
}
break;
default:
break;
}
}
}
MMputchar(CAN);
MMputchar(CAN);
MMputchar(CAN);
flushinput();
return "Remote did not respond"; // no sync
// send a packet
while(1) {
start_trans:
memset (xbuff, 0, X_BUF_SIZE); // start with an empty buffer
xbuff[0] = SOH; // copy the header
xbuff[1] = packetno;
xbuff[2] = ~packetno;
for(len = 0; len < 128 && !MMfeof(fnbr); len++) {
xbuff[len + 3] = MMfgetc(fnbr); // copy the data into the packet
}
if (len > 0) {
unsigned char ccks = 0;
for (i = 3; i < X_BLOCK_SIZE+3; ++i) {
ccks += xbuff[i];
}
xbuff[X_BLOCK_SIZE+3] = ccks;
// now send the block
for (retry = 0; retry < MAXRETRANS && !MMAbort; ++retry) {
// send the block
for (i = 0; i < X_BLOCK_SIZE+4 && !MMAbort; ++i) {
MMputchar(xbuff[i]);
}
// check the response
if ((c = _inbyte(DLY_1S)) >= 0 ) {
switch (c) {
case ACK:
++packetno;
goto start_trans;
case CAN: // canceled by remote
MMputchar(ACK);
flushinput();
return "Cancelled by remote";
break;
case NAK: // receiver got a corrupt block
default:
break;
}
}
}
// too many retrys... give up
MMputchar(CAN);
MMputchar(CAN);
MMputchar(CAN);
flushinput();
return "Too many errors in transmission";
}
// finished sending - send end of text
else {
for (retry = 0; retry < 10; ++retry) {
MMputchar(EOT);
if ((c = _inbyte((DLY_1S)<<1)) == ACK) break;
}
flushinput();
if(c == ACK) return "";
return "Error closing communications";
}
}
}
}
char *xmodemReceive(int fnbr) {
unsigned char xbuff[X_BUF_SIZE];
unsigned char *p;
unsigned char trychar = NAK; //'C';
unsigned char packetno = 1;
int i, c;
int retry, retrans = MAXRETRANS;
// first establish communication with the remote
while(1) {
for( retry = 0; retry < 16; ++retry) {
if(trychar) MMputchar(trychar);
if ((c = _inbyte((DLY_1S)<<1)) >= 0) {
switch (c) {
case SOH:
goto start_recv;
case EOT:
flushinput();
MMputchar(ACK);
return ""; // no more data
case CAN:
flushinput();
MMputchar(ACK);
return "Cancelled by remote";
break;
default:
break;
}
}
}
flushinput();
MMputchar(CAN);
MMputchar(CAN);
MMputchar(CAN);
return "Remote did not respond"; // no sync
start_recv:
trychar = 0;
p = xbuff;
*p++ = SOH;
for (i = 0; i < (X_BLOCK_SIZE+3); ++i) {
if ((c = _inbyte(DLY_1S)) < 0) goto reject;
*p++ = c;
}
if (xbuff[1] == (unsigned char)(~xbuff[2]) && (xbuff[1] == packetno || xbuff[1] == (unsigned char)packetno-1) && check(&xbuff[3], X_BLOCK_SIZE)) {
if (xbuff[1] == packetno) {
for(i = 0 ; i < X_BLOCK_SIZE ; i++)
MMfputc(xbuff[i + 3], fnbr);
++packetno;
retrans = MAXRETRANS+1;
}
if (--retrans <= 0) {
flushinput();
MMputchar(CAN);
MMputchar(CAN);
MMputchar(CAN);
return "Too many errors in transmission";
}
MMputchar(ACK);
continue;
}
reject:
flushinput();
MMputchar(NAK);
}
}
int xmodem_get(unsigned char *dest, int destsz)
{
unsigned char xbuff[1030]; /* 1024 for XModem 1k + 3 head chars + 2 crc + nul */
unsigned char *p;
int bufsz, crc = 0;
unsigned char trychar = 'C';
unsigned char packetno = 1;
int i, c, len = 0;
int retry, retrans = MAXRETRANS;
for (;;)
{
for ( retry = 0; retry < 160; ++retry)
{
if (trychar)
{
putchar(trychar);
// sleep(0x008f0000);
}
if ((c = try_getc((DLY_1S)<<1)) >= 0)
{
switch (c)
{
case SOH:
bufsz = 128;
goto start_recv;
case STX:
bufsz = 1024;
goto start_recv;
case EOT:
flushinput();
putchar(ACK);
return len; /* normal end */
case CAN:
if ((c = try_getc(DLY_1S)) == CAN)
{
flushinput();
putchar(ACK);
return -1; /* canceled by remote */
}
break;
default:
break;
}
}
}
if (trychar == 'C')
{
trychar = NAK;
continue;
}
flushinput();
putchar(CAN);
putchar(CAN);
putchar(CAN);
return -2; /* sync error */
start_recv:
if (trychar == 'C') crc = 1;
trychar = 0;
p = xbuff;
*p++ = c;
for (i = 0; i < (bufsz+(crc?1:0)+3); ++i)
{
if ((c = try_getc(DLY_1S)) < 0) goto reject;
*p++ = c;
}
if (xbuff[1] == (unsigned char)(~xbuff[2]) &&
(xbuff[1] == packetno || xbuff[1] == (unsigned char)packetno-1) &&
check(crc, &xbuff[3], bufsz))
{
if (xbuff[1] == packetno)
{
unsigned int count = destsz - len;
if (count > bufsz) count = bufsz;
if (count > 0)
{
//memcpy (&dest[len], &xbuff[3], count);
_writer(&xbuff[3], count);
len += count;
}
++packetno;
retrans = MAXRETRANS+1;
}
if (--retrans <= 0)
{
flushinput();
putchar(CAN);
putchar(CAN);
putchar(CAN);
return -3; /* too many retry error */
}
putchar(ACK);
continue;
}
reject:
flushinput();
putchar(NAK);
}
}
void event_loop (void (*act_on_button) (float x, float y),
void (*drawscreen) (void)) {
/* The program's main event loop. Must be passed a user routine *
* drawscreen which redraws the screen. It handles all window resizing *
* zooming etc. itself. If the user clicks a button in the graphics *
* (toplevel) area, the act_on_button routine passed in is called. */
XEvent report;
int bnum;
float x, y;
#define OFF 1
#define ON 0
turn_on_off (ON);
while (1) {
XNextEvent (display, &report);
switch (report.type) {
case Expose:
#ifdef VERBOSE
printf("Got an expose event.\n");
printf("Count is: %d.\n",report.xexpose.count);
printf("Window ID is: %d.\n",report.xexpose.window);
#endif
if (report.xexpose.count != 0)
break;
if (report.xexpose.window == menu)
drawmenu();
else if (report.xexpose.window == toplevel)
drawscreen();
else if (report.xexpose.window == textarea)
draw_message();
break;
case ConfigureNotify:
top_width = report.xconfigure.width;
top_height = report.xconfigure.height;
update_transform();
#ifdef VERBOSE
printf("Got a ConfigureNotify.\n");
printf("New width: %d New height: %d.\n",top_width,top_height);
#endif
break;
case ButtonPress:
#ifdef VERBOSE
printf("Got a buttonpress.\n");
printf("Window ID is: %d.\n",report.xbutton.window);
#endif
if (report.xbutton.window == toplevel) {
x = XTOWORLD(report.xbutton.x);
y = YTOWORLD(report.xbutton.y);
act_on_button (x, y);
}
else { /* A menu button was pressed. */
bnum = which_button(report.xbutton.window);
#ifdef VERBOSE
printf("Button number is %d\n",bnum);
#endif
button[bnum].ispressed = 1;
drawbut(bnum);
XFlush(display); /* Flash the button */
button[bnum].fcn(bnum, drawscreen);
button[bnum].ispressed = 0;
drawbut(bnum);
if (button[bnum].fcn == proceed) {
turn_on_off(OFF);
flushinput ();
return; /* Rather clumsy way of returning *
* control to the simulator */
}
}
break;
}
}
}
void typeline(bc *bc, char *preload,int echocr)
{
int i=0,j;
int code;
int backcount=0;
char linesave[LINESIZE],ch;
int linesin;
char ref;
int xdelta;
char *p1,*p2;
char token[128];
char *fake;
int scrollback;
int startx, starty;
char spaces[256], *zerospaces;
char *tail;
int oldlen;
memset(spaces, ' ', sizeof(spaces));
zerospaces = spaces + sizeof(spaces)-1;
*zerospaces = 0;
top:
tail="";
startx = bc->txpos;
starty = bc->typos;
xdelta=0;
linesin=bc->hcount>HISTSIZE ? HISTSIZE : bc->hcount;
strcpy(bc->debline, preload);
i=strlen(bc->debline);
tprintf(bc, preload);
ref=0;
fake=0;
scrollback=0;
while(!(bc->flags & (BF_CCHIT | BF_QUIT)))
{
if(!fake)
{
SDL_Delay(10);
scaninput(bc);
code=takedown(bc);
//if(code=='q' + MYALTED) exit(0); // alt-q
} else
{
code=*fake++;
if(!code) {fake=0;continue;}
}
if(code==-1) continue;
if(code==MYPAGEUP || code==(MYPAGEUP|MYSHIFTED))
{
if(code==MYPAGEUP) ++scrollback;
else scrollback+=bc->tysize;
scrollback=showhistory(bc, scrollback);
continue;
} else if(code==MYPAGEDOWN || code==(MYPAGEDOWN|MYSHIFTED))
{
if(code==MYPAGEDOWN) --scrollback;
else scrollback-=bc->tysize;
if(scrollback<0) scrollback=0;
scrollback=showhistory(bc, scrollback);
if(scrollback)
continue;
else
++ref;
}
if(code==9 || code==4)
{
j=0;
while(i+xdelta-j>0)
{
ch=bc->debline[i+xdelta-j-1];
if(!isalpha(ch) && !isdigit(ch) && ch!='_' && ch!='.') break;
++j;
}
p1=token;
while(j)
*p1++=bc->debline[i+xdelta-j--];
*p1=0;
if(*token)
{
if(code==9)
fake=complete(token);
else
{
cr(bc);
listall(token);
ref=1;
}
}
} else if(code==0x7f)
{
if(!xdelta) continue;
p1=bc->debline+i+xdelta;
p2=p1+1;
while((*p1++=*p2++));
--i;
++xdelta;
++ref;
} else if(code==MYLEFT)
{
if(i+xdelta>0) {--xdelta;++ref;}
} else if(code==MYRIGHT)
{
if(xdelta<0) {++xdelta;++ref;}
} else if(code==MYUP)
{
if(backcount<linesin)
{
if(!backcount)
memcpy(linesave,bc->debline,LINESIZE);
++backcount;
oldlen = strlen(bc->debline);
memcpy(bc->debline,
bc->debhist+LINESIZE*((bc->hcount-backcount) &
(HISTSIZE-1)), LINESIZE);
oldlen -= strlen(bc->debline);
if(oldlen>0) tail=zerospaces-oldlen;
xdelta=0;
}
++ref;
} else if(code==MYDOWN)
{
if(backcount)
{
--backcount;
oldlen = strlen(bc->debline);
if(!backcount) memcpy(bc->debline,linesave,LINESIZE);
else
memcpy(bc->debline,bc->debhist+LINESIZE*((bc->hcount-backcount) & (HISTSIZE-1)),LINESIZE);
oldlen -= strlen(bc->debline);
if(oldlen>0) tail=zerospaces-oldlen;
xdelta=0;
}
++ref;
} else if(code>=0 && code<128)
{
if(code==8)
{
if(i+xdelta)
{
--i;
p1=bc->debline+i+xdelta;
p2=p1+1;
while((*p1++=*p2++));
++ref;
} else continue;
} else if(code==CR)
{
if(echocr) cr(bc);
break;
}
else if(code>=0x20 && i<bc->txsize-1 && i<sizeof(bc->debline)-1)
{
p2=bc->debline+i;
p1=p2+1;
j=1-xdelta;
while(j--) *p1--=*p2--;
*p1=code;
++ref;
} else continue;
}
if(ref)
{
if(scrollback)
scrollback=showhistory(bc, 0);
i=strlen(bc->debline);
tprintf(bc, "\033%dx\033%dy%s %s\033%dx\033%dy",
startx, starty, bc->debline, tail, i+xdelta+startx, starty);
tail="";
ref=0;
}
}
if(bc->flags & BF_CCHIT)
{
flushinput(bc);
if(!(bc->flags & BF_RUNNING))
{
bc->flags &= ~BF_CCHIT;
preload="";
tprintf(bc, "\n");
goto top;
}
}
if(i)
{
memcpy(bc->debhist+LINESIZE*(bc->hcount & (HISTSIZE-1)),bc->debline,LINESIZE);
++bc->hcount;
}
}