void get_string(void)
{ char c, delim = loc[-1]; /* what started the string */
id_loc=id_first = &mod_text[1]; copy_char(delim);
if (delim=='L')
*id_loc++=delim=*loc++; /* after `\.L' comes the real delimiter */
else if (delim=='<') delim='>'; /* for file names in \&{\#include} lines */
do
{ if (loc>=limit)
{ err_print("! String didn't end"); loc=limit; break; }
copy_char(c=*loc++);
if (c=='\\')
if (loc<limit) copy_char(*loc++);
/* record `\.\\|c|' with |c!='\n'| literally */
else if (get_line())
if (program==cweave) --id_loc; /* |CWEAVE| erases backslash */
else copy_char('\n'); /* but |CTANGLE| copies escaped newline */
else
{ loc=buffer;
err_print("! Input ended in middle of string");
break;
}
else if (!including_header_file && c=='@')
if (*loc=='@') ++loc; /* undouble \:@ */
else err_print("! Double @ required in strings");
}
while (c!=delim);
if (id_loc>=mod_text_end)
{ print("\n! String too long: ");
term_write(mod_text+1,25); err_print("..");
}
}
bool get_get_param (void) {
if (* command != '?' && * command != '&') return false;
command++;
char * cp = key;
while (* command > 32 && * command != '=') copy_char (& cp, & command); * cp = '\0';
if (* command == '=') command++;
cp = area;
while (* command > 32 && * command != '&') copy_char (& cp, & command); * cp = '\0';
return true;
}
PrologElement * get_partial_request (void) {
skip_whitespaces ();
if (* command != '/') return 0;
command++;
int ap = 0; area [0] = '\0';
char * cp = area;
while (* command != '/' && * command != '?' && * command > 32) copy_char (& cp, & command);
* cp = '\0';
return interpret ();
}
bool get_param (void) {
if (key_pending [0] != '\0') {
strcpy (key, key_pending); strcpy (area, parameter_pending);
key_pending [0] = parameter_pending [0] = '\0';
return true;
}
if (* command <= 32) {skip_line (); return false;}
char * cp = key;
while (* command > 32 && * command != '=') copy_char (& cp, & command);
* cp = '\0';
if (strcmp (key, boundary) == 0) {
command = strstr (command, "name=");
if (command == 0) return false;
while (* command > 32 && * command != '"') command++; command++;
cp = key;
while (* command > 32 && * command != '"') * cp++ = * command++;
* cp = '\0';
if (strstr (command, "filename=") == command + 3) {
strcpy (key_pending, key); strcat (key_pending, "_filename");
char * sub1 = parameter_pending;
char * sub2 = command + 13;
while (* sub2 > 0 && * sub2 != '"') * sub1++ = * sub2++; * sub1 = '\0';
skip_line ();
}
skip_line ();
skip_line ();
cp = area;
char * terminator = strstr (command, boundary);
while (terminator != 0 && command < terminator - 2) * cp++ = * command++;
skip_line ();
* cp = '\0';
return true;
}
if (boundary [0] != '\0' && strstr (key, boundary) == key) return false;
if (* command == '=') command++;
cp = area;
while (* command > 32 && * command != '&') copy_char (& cp, & command);
* cp = '\0';
if (* command == '&') command++;
return true;
}
unsigned int ImageSplit(unsigned char *data,int width, int height){
int i,j,k;
int w,h;
int left,right;
int pixel_num = 0;
int top_height,bot_height;
int new_height = getImageHeight(data,width,height,&top_height,&bot_height);
int l_width = ((width*3+3)>>2)<<2;
float calc_out[ANN_OUTPUT_NUM];
int calc_iout[ANN_OUTPUT_NUM];
unsigned char recogArr[13]={0};
int index = 0;
left = right = 0;
while(1){
if (left >= width){
break;
}
while(left < width){
pixel_num = 0;
for (i=0; i<height; i++){/*scan from bottom to top*/
k = i*l_width + left*3;
if (data[k] == 0 && data[k+1] == 0 && data[k+2] == 0){
pixel_num ++;
}
}
if (pixel_num <= 1){
left ++;
}
else{
break;
}
}
right = left + 1;
if (right >= width){
break;
}
while(right < width){
pixel_num = 0;
for (i=0;i<height; i++){
k = i*l_width + right*3;
if (data[k] == 0 && data[k+1] == 0 && data[k+2] == 0){
pixel_num ++;
}
}
if (pixel_num > 1){
right++;
}
else{
break;
}
}
if (right >= width){
break;
}
if ((right-left) <= 2){
left = right + 1;
continue;
}
if (IsHorizonLine(data,left,right,width,height) == 1){ /* symbol "-" ? */
left = right + 1;
continue;
}
set_verticalbar_blue(data,width,height,left,right-1);
#if 1
int recogNum = 0;
if ((right-left) <= MAX_CHAR_WIDTH){
int top_pos = 0;
int bot_pos = 0;
// int left_pos = 0;
// int right_pos = 0;
getSlicedHeight(data,left,right,width,height,&top_pos,&bot_pos);
// getSlicedWidth(data,left,right,width,height,&left_pos,&right_pos);
// unsigned char *one_ch = new unsigned char[(right-left)*(top_height-bot_height+1)];
unsigned char *one_ch = new unsigned char[(right-left + 1)*(top_pos-bot_pos+1)];
if (one_ch == NULL){
printf("(%d) allocate memory failed\n",__LINE__);
}
copy_char(data,one_ch,left,right,top_pos,bot_pos,width);
unsigned char *norm_data = new unsigned char[NORM_WIDTH*NORM_HEIGHT];
if (norm_data == NULL){
printf("(%d) allocate memory failed\n",__LINE__);
}
// norm_data = ImageNorm(one_ch,right-left,top_height-bot_height+1);
norm_data = ImageNorm(one_ch,norm_data,right - left+1, top_pos-bot_pos+1);
// ImageThinning(norm_data,NORM_WIDTH,NORM_HEIGHT);
float *feature_vector = new float[MAX_FEATURE_LEN];
if (feature_vector == NULL){
printf("(%d) allocate memory failed\n",__LINE__);
}
memset(feature_vector,0,MAX_FEATURE_LEN);
getfeatureVector(norm_data,feature_vector,NORM_WIDTH,NORM_HEIGHT);
#if 1
PRINT_NORM(norm_data,NORM_WIDTH,NORM_HEIGHT);
PRINT_FEATURE(feature_vector,MAX_FEATURE_LEN);
#endif
recogDigital(feature_vector,&calc_out[0]);
printf("%f %f %f %f\n",calc_out[0],calc_out[1],calc_out[2],calc_out[3]);
for (i=0; i<4; i++){
if (fabs(calc_out[i]) > 0.5){
calc_iout[i] = 1;
}
else{
calc_iout[i] = 0;
}
}
printf("%d %d %d %d\n",calc_iout[0],calc_iout[1],calc_iout[2],calc_iout[3]);
recogNum = (calc_iout[0]<<3)+(calc_iout[1]<<2) + (calc_iout[2]<<1) + calc_iout[3];
if (recogNum > 9){
printf("recognized failure(recogNum = %d)\n",recogNum);
recogArr[index]='X';
index++;
// exit(1);
}
else{
printf("%d\n",recogNum);
recogArr[index]=recogNum;
index++;
}
#if 1
set_verticalbar_blue(data,width,height,left,right-1);
#endif
delete[] one_ch;
delete[] norm_data;
delete[] feature_vector;
}
else{
#if 1
int new_left = left;
int new_right = new_left + MIN_WINDOW_LEN;
int loop = 0;
while(new_right < right){
int recog_sliced = 0;
int temp_left = 0;
int temp_right = 0;
// printf("new_left =%d, new_right=%d,left=%d,right=%d\n",new_left,new_right,left,right);
if ((new_right - new_left) == MIN_WINDOW_LEN){
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",new_left,new_right,left,right);
if (IsHorizonLine(data,new_left,new_right,width,height) == 1){
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,new_left,new_right,top_height, bot_height, width,height);
if (recog_sliced != 1){
temp_left = new_left -1;
temp_right = new_right -1;
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
if (IsHorizonLine(data,temp_left,temp_right,width,height) == 1){
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if (recog_sliced != 1){
temp_left = new_left + 1;
temp_right = new_right + 1;
if (temp_right >= right){
new_right = right;/*do nothing, end this while loop*/
}
else{
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
if (IsHorizonLine(data,temp_left,temp_right,width,height) == 1){
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if (recog_sliced != 1){
//new_right = new_left + MAX_WINDOW_LEN;
//if (new_right >= right){
// new_right = right -1;
//}
new_right = new_left + MIN_WINDOW_LEN + 1;
}
else{
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
//new_left = new_right + 1;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN ;
/*go to next loop*/
}
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index++;
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*if new_right > right, end this while loop*/
}
}
if ((new_right - new_left) == (MIN_WINDOW_LEN + 1)){
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",new_left,new_right,left,right);
if (IsHorizonLine(data,new_left,new_right,width,height) == 1){
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,new_left,new_right,top_height, bot_height, width,height);
if (recog_sliced != 1){
temp_left = new_left - 1;
temp_right = new_right - 1;
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
if (IsHorizonLine(data,temp_left,temp_right,width, height) == 1){
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if (recog_sliced != 1){
temp_left = new_left + 1;
temp_right = new_right + 1;
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
if (temp_right >= right){
new_right = right; /*do nothing, just end this loop*/
}
else{
if (IsHorizonLine(data,temp_left,temp_right,width,height) == 1){
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
continue;
}
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if (recog_sliced != 1){
new_right = new_left + MAX_WINDOW_LEN;
if (new_right >= right){
new_right = right - 1;
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
}
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index ++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN; /*if new_right > right,just end this loop*/
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index++;
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
}
}
if ((new_right - new_left) > (MIN_WINDOW_LEN+1) && (new_right - new_left) <= MAX_WINDOW_LEN){
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",new_left,new_right,left,right);
recog_sliced = recog_one_sliced(data,new_left,new_right,top_height,bot_height,width,height);
if ((recog_sliced == 1 || recog_sliced < 0 || recog_sliced >= 10) /*|| (index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*failed*/
temp_left = new_left -1;
temp_right = new_right -1;
/*recognize again*/
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if ((recog_sliced < 0 || recog_sliced >= 10)/* ||(index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*failed again*/
temp_left = new_left + 1;
temp_right = new_right + 1;
if (temp_right >= right){
temp_right = right -1;
}
/*the last try*/
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if (( recog_sliced < 0 || recog_sliced >= 10) /*||(index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*still failed*/
/*keep new_left unchange*/
new_right = new_left + (MAX_WINDOW_LEN + 1);
if (new_right >= right){
new_right ++;/*here just end this loop*/
}
}
else{
/*success*/
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*go to next loop*/
}
}
else{
/*success*/
printf("%d\n",recog_sliced);
recogArr[index] = recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*go to next loop*/
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*go to next while loop. if new_right > right, just stop this while loop*/
}
}
if ((new_right - new_left) == (MAX_WINDOW_LEN + 1)){
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",new_left,new_right,left,right);
recog_sliced = recog_one_sliced(data,new_left,new_right,top_height,bot_height,width,height);
if ((recog_sliced < 0 || recog_sliced >= 10) /*|| (index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*failed*/
temp_left = new_left - 1;
temp_right = new_right -1;
/*recognize again*/
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if ((recog_sliced < 0 || recog_sliced >= 10) /*|| (index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*failed again*/
temp_left = new_left + 1;
temp_right = new_right + 1;
if (temp_right >= right){
temp_right = right -1;
}
/*last recog try*/
printf("new_left=%d,new_right=%d,left=%d,right=%d\n",temp_left,temp_right,left,right);
recog_sliced = recog_one_sliced(data,temp_left,temp_right,top_height,bot_height,width,height);
if ((recog_sliced == 1 || recog_sliced < 0 || recog_sliced >= 10) /*|| (index == 1 && (recog_sliced != 3 || recog_sliced != 5 || recog_sliced != 8))*/){
/*totally failed*/
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*do not do it again*/
printf("%d:recog given up\n",__LINE__);
recogArr[index]='X';
index++;
}
else{
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*go to next loop*/
}
}
else{
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
new_left = temp_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
}
}
else{
/*success*/
printf("%d\n",recog_sliced);
recogArr[index]=recog_sliced;
index++;
new_left = new_right + 1;
new_right = new_left + MIN_WINDOW_LEN;
/*if new_right >= right ,just end this loop*/
}
}
}
#endif
}
#endif
left = right;
}
for (i=0; i<index; i++){
if (recogArr[i] !='X'){
printf("%d",recogArr[i]);
}
else{
printf("%c",recogArr[i]);
}
}
printf("\n");
}
void featureExtract(unsigned char *data,int width, int height)
{
int i=0;
int j=0;
int k=0;
float calc_out[ANN_OUTPUT_NUM];
int calc_iout[ANN_OUTPUT_NUM];
int l_width = ((width*3 + 3)>>2)<<2;
unsigned char *norm_data = new unsigned char[NORM_WIDTH*NORM_HEIGHT];
for (i=0; i<width; i++){
for (j=MIN_WINDOW_LEN; j<= MAX_WINDOW_LEN; j++){
int new_left = i;
int new_right = i+j;
int top_height = 0;
int bot_height = 0;
getSlicedHeight(data,new_left,new_right,width,height,&top_height,&bot_height);
printf("left=%d,right=%d,top=%d,bot=%d\n",new_left,new_right,top_height,bot_height);
unsigned char *one_ch = new unsigned char[(new_right-new_left + 1)*(top_height-bot_height+1)];
copy_char(data,one_ch,new_left,new_right,top_height,bot_height,width);
ImageNorm(one_ch,norm_data,new_right - new_left+1, top_height-bot_height+1);
float *feature_vector = new float[MAX_FEATURE_LEN];
memset(feature_vector,0,MAX_FEATURE_LEN);
getfeatureVector(norm_data,feature_vector,NORM_WIDTH,NORM_HEIGHT);
int index = 0;
float maxsim=getsimvalue(feature_vector,10,144,&index);
recogDigital(feature_vector,&calc_out[0]);
//printf("calc_out[0]=%0.3f,calc_out[1]=%0.3f,calc_out[2]=%0.3f,calc_out[3]=%0.3f\n",calc_out[0],calc_out[1],calc_out[2],calc_out[3]);
PRINT_NORM(norm_data,NORM_WIDTH,NORM_HEIGHT);
PRINT_FEATURE(feature_vector,MAX_FEATURE_LEN);
printf("calc_out[0]=%0.3f,calc_out[1]=%0.3f,calc_out[2]=%0.3f,calc_out[3]=%0.3f\n",calc_out[0],calc_out[1],calc_out[2],calc_out[3]);
/*check calc_out*/
int flag = 1;
for (k=0; k<4; k++){
if (calc_out[k] <= -0.1){
printf("refused\n");
flag = 0;
break;
}
else if (calc_out[k] >= 0.1 && calc_out[k] < 0.85){
printf("refused\n");
flag = 0;
break;
}
}
if (flag == 1){
int recogNUM = 0;
for (k=0; k<4; k++){
if (fabs(calc_out[k]) < 0.1){
recogNUM = 2*recogNUM;
}
else{
recogNUM = 2*recogNUM + 1;
}
}
printf("recogNUM=%d\n",recogNUM);
}
printf("maxsim=%f,index=%d,train_result=%d\n",maxsim,index,train_result[index]);
}
}
}
int recog_one_sliced(unsigned char *data,int sliced_left, int sliced_right, int top_height, int bot_height, int image_width, int image_height)
{
int i;
int recogNum = 0;
float calc_out[ANN_OUTPUT_NUM];
int left_pos = 0;
int right_pos = 0;
int top_pos = 0;
int bot_pos = 0;
// getSlicedWidth(data,sliced_left,sliced_right,image_width,image_height,&left_pos,&right_pos);
getSlicedHeight(data,sliced_left,sliced_right,image_width,image_height,&top_pos,&bot_pos);
// unsigned char *sliced = new unsigned char[(sliced_right - sliced_left + 1)*(top_height - bot_height + 1)];
unsigned char *sliced = new unsigned char[(sliced_right - sliced_left + 1)*(top_pos - bot_pos + 1)];
if (sliced == NULL){
printf("(line=%d)allocate memory failure!\n",__LINE__);
exit(1);
}
// copy_char(data,sliced,sliced_left,sliced_right,top_height,bot_height,image_width);
copy_char(data,sliced,sliced_left,sliced_right,top_pos,bot_pos,image_width);
unsigned char *norm_data = new unsigned char[NORM_WIDTH*NORM_HEIGHT];
// norm_data = ImageNorm(sliced,sliced_right - sliced_left + 1,top_height - bot_height + 1);
norm_data = ImageNorm(sliced,norm_data,sliced_right - sliced_left + 1, top_pos - bot_pos + 1);
// ImageThinning(norm_data,NORM_WIDTH,NORM_HEIGHT);
delete[] sliced;
float *feature_vector = new float[MAX_FEATURE_LEN];
if (feature_vector == NULL){
printf("(line=%d)allocate memory failure!\n",__LINE__);
exit(1);
}
memset(feature_vector,0,MAX_FEATURE_LEN);
getfeatureVector(norm_data,feature_vector, NORM_WIDTH,NORM_HEIGHT);
PRINT_NORM(norm_data,NORM_WIDTH,NORM_HEIGHT);
PRINT_FEATURE(feature_vector,MAX_FEATURE_LEN);
recogDigital(feature_vector,&calc_out[0]);
printf("%f %f %f %f\n",calc_out[0],calc_out[1],calc_out[2],calc_out[3]);
/*check ANN output*/
#if 0
int neg_num = 0;
for (i = 0; i<4; i++){
if (calc_out[i] < -0.2){
return -1;
}
else if (calc_out[i] < -0.1 && calc_out[i] >= -0.2){
neg_num ++;
if (neg_num >=2){
return -1;
}
}
else if (calc_out[i] > 0 && fabs(calc_out[i] - 0.5) <= 0.25){
return -1;
}
}
#endif
for (i=0; i<4; i++){
if (calc_out[i] < (-0.2)){
printf("calc_out[%d]=%f\n",i,calc_out[i]);
return -1;
}
else if (calc_out[i] >= 0.25 && calc_out[i] <= 0.75){
printf("calc_out[%d]=%f\n",i,calc_out[i]);
return -1;
}
}
for (i=0; i<4; i++){
if (fabs(calc_out[i]) > 0.5){
recogNum = 2*recogNum + 1;
}
else{
recogNum = 2*recogNum;
}
}
printf("recogNum=%d\n",recogNum);
return recogNum;
}
Alignment* copy_aln ( Alignment *A, Alignment *B)
{
int a, b;
int nnseq;
int nlen;
/* c[100]=10;*/
if ( A==NULL){free_aln(B); return NULL;}
nnseq=MAX(A->nseq, A->max_n_seq);
nlen=A->len_aln+1;
if (B)
B=realloc_alignment2 (B, nnseq, nlen);
else
B=declare_aln2 (nnseq, nlen);
B->S=A->S;
/*SIZES*/
B->max_len=A->max_len;
B->min_len=A->min_len;
B->declared_len=nlen;
B->max_n_seq=nnseq;
B->nseq=A->nseq;
B->len_aln=A->len_aln;
/*sequence Information*/
if ( A->generic_comment)
{
vfree(B->generic_comment);
B->generic_comment=vcalloc (strlen(A->generic_comment)+1, sizeof (char));
sprintf ( B->generic_comment, "%s", A->generic_comment);
}
if ( (A->S)==NULL){vfree (B->len); B->len=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int ( A->len, B->len, B->nseq);
B->seq_comment=copy_char ( A->seq_comment, B->seq_comment, -1,-1);
B->aln_comment=copy_char ( A->aln_comment, B->aln_comment, -1,-1);
B->name=copy_char ( A->name, B->name, -1,-1);
B->file=copy_char ( A->file, B->file, -1,-1);
B->tree_order=copy_char ( A->tree_order, B->tree_order, -1,-1);
B->expanded_order=A->expanded_order;
free_char ( B->seq_al, -1);
B->seq_al=declare_char(B->max_n_seq, B->declared_len);
// HERE ("A: MAX_NSEQ=%d %d %d %d",B->nseq, B->max_n_seq, B->declared_len, B->len_aln);
// HERE ("B: MAX_NSEQ=%d %d %d %d",A->nseq, A->max_n_seq, A->declared_len, A->len_aln);
for ( a=0; a< nnseq; a++)
{
if (A->seq_al[a])
{
for ( b=0; b< A->len_aln; b++)
B->seq_al[a][b]=A->seq_al[a][b];
}
}
B->order=copy_int ( A->order, B->order, -1, -1);
B->S=A->S;
if (A->seq_cache)
{
B->seq_cache=copy_int ( A->seq_cache, B->seq_cache,-1,-1);
}
if (A->cdna_cache)
{
B->cdna_cache=copy_int ( A->cdna_cache, B->cdna_cache,-1,-1);
}
B->P=copy_profile (A->P);
B->Dp_result=A->Dp_result;
/*Score*/
if ( (A->S)==NULL){vfree (B->score_seq); B->score_seq=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int( A->score_seq,B->score_seq,B->nseq);
B->score_res=A->score_res;
B->score_aln=A->score_aln;
B->score=A->score;
B->ibit=A->ibit;
B->cpu=A->cpu;
B->finished=A->finished;
/*Output Options*/
B->output_res_num=A->output_res_num;
B->residue_case=A->residue_case;
B->expand=A->expand;
B->CL=A->CL;
B->random_tag=A->random_tag;
/*Make the function Recursive */
if ( A->A)
{
B->A=copy_aln (A->A, NULL);
}
else B->A=NULL;
return B;
}
