int hpx_main()
{
{
std::vector<int> keys =
{
1, 4, 2, 8, 5, 7, 1, 4, 2, 8, 5, 7,
1, 4, 2, 8, 5, 7, 1, 4, 2, 8, 5, 7,
1, 4, 2, 8, 5, 7, 1, 4, 2, 8, 5, 7
};
std::vector<char> values =
{
'a', 'b', 'c', 'd', 'e', 'f', 'a', 'b', 'c', 'd', 'e', 'f',
'a', 'b', 'c', 'd', 'e', 'f', 'a', 'b', 'c', 'd', 'e', 'f',
'a', 'b', 'c', 'd', 'e', 'f', 'a', 'b', 'c', 'd', 'e', 'f'
};
hpx::cout << "unsorted sequence: {";
print_sequence(keys, values);
hpx::parallel::sort_by_key(
hpx::parallel::par,
keys.begin(),
keys.end(),
values.begin());
hpx::cout << "sorted sequence: {";
print_sequence(keys, values);
}
return hpx::finalize();
}
void print_sorted_alignment(sorted_alignment_block aln){
if(aln==NULL) return;
printf("\na %s\n", aln->data);
int i =0;
for(;i<aln->in_size; ++i) print_sequence(aln->in_sequences[i]);
for(i=0; i < aln->out_size; ++i) print_sequence(aln->out_sequences[i]);
}
int main(int argc, char *argv[])
{
int sequence[] = {3, 3242, 21, 55, 653, 19, 139, 459, 138, 45349, 19, 2, 1};
int sequence_length = sizeof(sequence)/sizeof(sequence[0]);
printf("Sorting %d values in sequence ", sequence_length);
print_sequence(sequence, sequence_length);
/* Insertion Sort */
int marker, key_index, key;
for (key_index = 1; key_index < sequence_length; key_index++) { // traverse sequence, start at 2nd index
key = sequence[key_index];
marker = key_index - 1; // set marker at first index left of current key index
while (marker > -1 && sequence[marker] > key) {
sequence[marker+1] = sequence[marker]; // if marker val greater than key, shift right
marker = marker - 1; // count left while current marker val is greater than key
}
sequence[marker+1] = key; // replace key
}
printf("Done sorting into result sequence ");
print_sequence(sequence, sequence_length);
return 0;
}
int main() {
/* integers all must have the same amount of digits */
int seq[SEQUENCE_LENGTH] = {7325, 1334, 4432, 5991, 1324, 8421, 5838, 3492, 6539, 3591};
print_before_message();
print_sequence(seq);
radix_sort(seq);
print_after_message();
print_sequence(seq);
}
void init_screen(uint8_t i2c_address)
{
//_delay_ms(110); //TOO FAST, WILL NOT TURN ON.
//_delay_ms(115); //WORKS
//_delay_ms(112); //SOMETIMES WORKED THEN STOPPED WORKING
_delay_ms(150);
print_sequence(init_sequence,i2c_address);
}
void cq(int sum) {
if (sum < 3) return;
int small = 1;
int big = 2;
int mid = (sum + 1)/2;
int cur_sum = small + big;
while (small < mid) {
if (cur_sum == sum) {
print_sequence(small, big);
}
while (cur_sum > sum && small < mid) {
cur_sum -= small;
small++;
if (cur_sum == sum) print_sequence(small, big);
}
big++;
cur_sum += big;
}
return;
}
int main(int argc, char *argv[])
{
int sequence[] = {3, 3242, 21, 55, 653, 19, 139, 459, 138, 45349, 19, 2, 1};
int sequence_length = sizeof(sequence)/sizeof(sequence[0]);
printf("Sorting %d values in sequence ", sequence_length);
print_sequence(sequence, sequence_length);
insertion_sort(sequence, sequence_length);
printf("Done sorting. Result ");
print_sequence(sequence, sequence_length);
printf("Testing if result sort is valid....");
int pass = test_insertion_sort(sequence, sequence_length);
if (pass)
printf("Yes!\n");
else
printf("No!\n");
return 0;
}
void print_hash_alignment(hash_alignment_block aln){
if(aln==NULL) return;
printf("\na %s\n",aln->data);
ENTRY *ret_val;
int hc=0;
for(int i = 0; i < aln->size; ++i){
ENTRY search={aln->species[i],NULL};
hc = hsearch_r(search,FIND,&ret_val,aln->sequences);
if(hc == 0){
fprintf(stderr,"Failed to read hash table: %s\n", strerror(errno));
exit(1);
}
if(ret_val != NULL) print_sequence(ret_val->data);
}
}
void radix_sort(int *seq) {
int i, j, h;
int bucket[10][SEQUENCE_LENGTH];
int largest;
int n_digits;
largest = largest_number_in_sequence(seq);
n_digits = how_many_digits_in_number(largest);
for (i = (n_digits - 1); i >= 0; i--) {
zero_out_bucket(bucket);
populate_bucket(i, seq, bucket);
restore_bucket_to_seq(seq, bucket);
printf("Sequence after sorting %dth digit\n", i);
print_sequence(seq);
}
}
/* used in window-mode to shift the input sequence */
void shift_input(toptions *opts, tsequence *seq, char output){
int i;
/* printf("window_pos: %d\n", opts->window_pos); */
/* printf("window_size: %d\n", opts->window_size); */
/* printf("seq->seq: %s\n", seq->seq); */
/* printf("seq->original_seq: %s\n", seq->original_seq); */
for (i=opts->window_pos; i<=opts->window_pos + opts->window_size; i++)
seq->seq[i-opts->window_pos] = seq->original_seq[i];
if (number_of_graphics) {
for (i=opts->window_pos; i<=opts->window_pos + opts->window_size; i++)
graphics_sequence[i-opts->window_pos] = seq->original_seq[i];
graphics_sequence[strlen(seq->seq)] = 0;
}
convert_input(0, seq->seq, opts->window_size);
if (output) print_sequence(opts, seq, opts->window_pos, opts->window_size);
}
void rna_output_subopt_start(toptions *opts, tsequence *seq, char *algebra, int result_score, int range_begin, int range_end)
{
if (!opts->window_mode && (strcmp(algebra, "count"))) {
printf("Suboptimal range: [%.2f kcal/mol - %.2f kcal/mol]\n", ((float) range_begin)/100, ((float) range_end)/100);
printf("\n");
if (seq->descr && seq->descr[0]) {
pcolor(opts->colored_output,COLOR_BOLD);
printf(">%s", seq->descr);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\n");
}
if (!opts->split_output_mode) printf("%s\n", seq->original_seq);
}
// print subsequence for first window iteration
// for later iterations, this is done in function shift_input
if (opts->window_mode && (opts->window_pos==0) && (strcmp(algebra, "count"))) {
print_sequence(opts, seq, opts->window_pos, opts->window_size);
}
}
int4 main(int4 argc, char* argv[])
{
// User must provide FASTA format file at command line
if (argc < 4)
{
fprintf(stderr, "Useage: indexdb <DB filename> <Query Length> <Number of Sequences>\n");
exit(-1);
}
char *filename = argv[1];
int queryLen = atoi(argv[2]);
int numSeqs = atoi(argv[3]);
// Open sequence data file and read information
encoding_initialize(encoding_protein);
readdb_open_mem(filename);
int ii;
//int interval = readdb_numberOfSequences / numSeqs;
int queryCnt = 0;
for(ii = 0; ii < readdb_numVolumeSequences && queryCnt < numSeqs; ii++)
{
if(readdb_sequenceData[ii].sequenceLength >= queryLen)
{
print_sequence(ii);
if(queryCnt < 50)
fprint_sequence(ii, queryCnt + 1);
queryCnt++;
}
}
fprintf(stderr, "maxQueryLength: %d\n", readdb_sequenceData[ii].sequenceLength);
//close database
readdb_close_mem();
return 0;
}
void assembly_run(Params *p, double nfert, double **regpool, int poolsize, char *folder, char *replicate_identity)
{
// Define and initialize the history and ecosystem lists
//------------------------------------------------------
sll history;
sll_init(&history,(void*)free_seq);
sll ecosys;
sll_init(&ecosys,(void*)free_species);
// create the basal resources
//---------------------------
basal(p,&ecosys,nfert);
// create and initialize the presence matrix (ne pas oublier de mettre les espèces au minimum pour l'invasion)
//------------------------------------------
unsigned int **presence = (unsigned int**)mat_alloc(2,poolsize,sizeof(unsigned int));
for(int i = 0 ; i < poolsize ; ++i)
{
presence[0][i] = regpool[i][1];
presence[1][i] = 0;
}
// get the initial values of the sequence
//---------------------------------------
seqlevel *seq0 = fill_seq(&ecosys,0,0);
seq0->success = 0;
sll_add_head(&history,seq0);
// assemble until any species can install (or all are already installed)
//----------------------------------------------------------------------
int a = poolsize + EAM_NBNUT + EAM_NBDET; /* expected ecosystem size */
int stop_endcycles = poolsize * EAM_STOP_ENDCYCLE; /* variable to stop the sequence if infinite */
int endcycles = 0; /* 0 if endpoint / 1 if endcycle */
int unsucc = EAM_STOP; /* check the success of the invader */
int invasion = 1; /* invasion number */
while(ecosys.length != a)
{
int b = get_int(p->rng,0,poolsize); /* select randomly the number of the species in the regional pool */
if(presence[1][b] == 0) /* if the species is not already in the ecosystem */
{
ParamSP *sp = (ParamSP*)malloc(sizeof(ParamSP));
tr_sp_struct(regpool[b],sp);
install_process(p,&ecosys,sp); /* install the species */
seqlevel *seq = fill_seq(&ecosys,invasion,presence[0][b]); /* create and initialize a sequence node */
sll_rm(&ecosys,extinct_condition); /* remove the extincted species */
presence_absence(&ecosys,presence,poolsize); /* fill the presence-absence matrix */
unsucc = (presence[1][b] == 0) ? unsucc-1 : EAM_STOP; /* upgrade the counter of unsuccessfull installations */
seq->success = presence[1][b]; /* fill the success of invader installation in the sequence node */
sll_add_head(&history,seq); /* add the sequence node to the assembly history */
++invasion; /* upgrade the invasion number */
--stop_endcycles; /* upgrade the endcycle detector */
}
if(unsucc == 0) break;
if(stop_endcycles == 0) /* break the loop if its an endcycle */
{
endcycles = 1;
break;
}
}
// print the outputs : subpool / final community / sequence / abundances history / identity history
//------------------
print_final_community(&ecosys,folder,replicate_identity);
print_id_history(&history,poolsize,folder,replicate_identity);
print_final_biomasses_history(&history,poolsize,folder,replicate_identity);
print_sequence(&history,folder,replicate_identity);
char *buffer = (char*)malloc(100);
sprintf(buffer, "%s/%s_endcycle.txt",folder,replicate_identity);
FILE *out = fopen(buffer,"w");
fprintf(out,"%d",endcycles);
fclose(out);
// free the memory
//----------------
mat_free((void**)presence,2);
sll_rm_all(&history);
sll_rm_all(&ecosys);
free(buffer);
}
void edit_sequence(char s[], char t[]) {
int m = strlen(s);
int n = strlen(t);
int i, j;
int i_cost, d_cost, s_cost;
edit_struct a[MAX_LEN][MAX_LEN];
a[0][0].p_i = -1;
a[0][0].p_j = -1;
a[0][0].op = '\0';
a[0][0].edit_dist = 0;
for(i = 1; i <= m; i++) {
a[i][0].p_i = i-1;
a[i][0].p_j = 0;
a[i][0].op = 'd';
a[i][0].edit_dist = i;
}
for(j = 1; j <= n; j++) {
a[0][j].p_i = 0;
a[0][j].p_j = j-1;
a[0][j].op = 'i';
a[0][j].edit_dist = j;
}
for(i = 1; i <= m; i++) {
for(j = 1; j <= n; j++) {
i_cost = a[i][j-1].edit_dist + insert_cost(t[j-1]);
d_cost = a[i-1][j].edit_dist + delete_cost(s[i-1]);
s_cost = a[i-1][j-1].edit_dist + substitute_cost(s[i-1], t[j-1]);
if(i_cost <= d_cost) {
if(i_cost <= s_cost) {
a[i][j].p_i = i;
a[i][j].p_j = j-1;
a[i][j].op = 'i';
a[i][j].edit_dist = i_cost;
}
else {
a[i][j].p_i = i-1;
a[i][j].p_j = j-1;
if(substitute_cost(s[i-1], t[j-1]))
a[i][j].op = 's';
else
a[i][j].op = 'm';
a[i][j].edit_dist = s_cost;
}
}
else {
if(d_cost <= s_cost) {
a[i][j].p_i = i-1;
a[i][j].p_j = j;
a[i][j].op = 'd';
a[i][j].edit_dist = d_cost;
}
else {
a[i][j].p_i = i-1;
a[i][j].p_j = j-1;
if(substitute_cost(s[i-1], t[j-1]))
a[i][j].op = 's';
else
a[i][j].op = 'm';
a[i][j].edit_dist = s_cost;
}
}
}
}
printf("%d\n", a[m][n].edit_dist);
print_sequence(a, m, n);
printf("\n");
}
void print_sequence(edit_struct a[][MAX_LEN], int i, int j) {
if(i == 0 && j == 0) return;
print_sequence(a, a[i][j].p_i, a[i][j].p_j);
printf("%c", a[i][j].op);
}
inline Ostream& operator <<(Ostream& os, const std::forward_list<T, A>& x)
{
return print_sequence(os, x.begin(), x.end());
}
inline Ostream& operator <<(Ostream& os, const std::array<T, N>& x)
{
return print_sequence(os, x.begin(), x.end());
}
void print_alignment(alignment_block aln){
if(aln==NULL)return;
printf("\na %s\n",aln->data);
for(int i=0; i < aln->size; ++i)
if(aln->sequences[i] != NULL) print_sequence(aln->sequences[i]);
}
int main(void)
{
int n, m;
int l1, l2;
scanf("%d %d", &n, &m);
while(n!= 0 || m != 0)
{
int i,j;
int sum = 0;
int flag = 0;
int step = 0;
char s[5];
for(i = 0; i < n; ++i)
for(j = 0; j < n; ++j)
map[i][j] = 0;
for(i = 0; i < m; ++i)
{
scanf("%s", s);
int x, y;
x = s[0] - 'A';
y = s[2] - 'A';
if(map[y][x] != 0)
{
flag = 2;
step = i + 1;
break;
}
if(map[x][y] == 0)
{
map[x][y] = 1;
sum++;
int i1, i2;
for(i1 = 0 ; i1 < n; ++i1)
{
if(map[i1][x] != 0)
{
if(map[y][i1] == 1)
{
flag = 2;
step = i + 1;
break;
}
if(map[i1][y] == 0)
{
sum++;
map[i1][y] = 1;
}
}
}
for(i2 = 0; i2 < n; ++i2)
{
if(map[y][i2] != 0)
{
if(map[i2][x] == 1)
{
flag = 2;
step = i + 1;
break;
}
if(map[x][i2] == 0)
{
sum++;
map[x][i2] = 1;
}
}
}
for(i1 = 0; i1 < n; ++i1)
{
for(i2 = 0; i2 < n; ++i2)
{
if(map[i1][x] != 0 && map[y][i2] != 0)
{
if(map[i2][i1] != 0)
{
flag = 2;
step = i + 1;
break;
}
if(map[i1][i2] == 0)
{
sum ++;
map[i1][i2] = 1;
}
}
}
if(flag == 2)
break;
}
}
if(flag == 2)
break;
if(sum == n * (n - 1) / 2 && flag == 0)
{
flag = 1;
step = i + 1;
break;
}
/*
for(l1 = 0; l1 < n; ++l1)
{
for(l2 = 0; l2 < n; ++l2)
{
printf("%d ", map[l1][l2]);
}
printf("\n");
}*/
}
/*
for(l1 = 0; l1 < n; ++l1)
{
for(l2 = 0; l2 < n; ++l2)
{
printf("%d ", map[l1][l2]);
}
printf("\n");
}*/
for(i = i + 1; i < m; ++i)
{
scanf("%s", s);
}
switch(flag)
{
case 0: printf("Sorted sequence cannot be determined.\n");break;
case 1: printf("Sorted sequence determined after %d relations: ", step);
print_sequence(n);
break;
case 2: printf("Inconsistency found after %d relations.\n", step);
}
scanf("%d %d", &n, &m);
}
return 0;
}
