int main(int argc, char *argv[]) {
int i;
Table_T identifiers = Table_new(0, NULL, NULL);
for (i = 1; i < argc; i++) {
FILE *fp = fopen(argv[i], "r");
if (fp == NULL) {
fprintf(stderr, "%s: can't open '%s' (%s)\n",
argv[0], argv[i], strerror(errno));
return EXIT_FAILURE;
} else {
xref(argv[i], fp, identifiers);
fclose(fp);
}
}
if (argc == 1) xref(NULL, stdin, identifiers);
{
int i;
void **array = Table_toArray(identifiers, NULL);
qsort(array, Table_length(identifiers),
2*sizeof (*array), compare);
for (i = 0; array[i]; i += 2) {
printf("%s", (char *)array[i]);
print(array[i+1]);
}
FREE(array);
}
return EXIT_SUCCESS;
}
void print(Table_T files) {
int i;
void **array = Table_toArray(files, NULL);
qsort(array, Table_length(files), 2*sizeof (*array),
compare);
for (i = 0; array[i]; i += 2) {
if (*(char *)array[i] != '\0')
printf("\t%s:", (char *)array[i]);
{
void **lines = Set_toArray(array[i+1], NULL);
qsort(lines, Set_length(array[i+1]), sizeof (*lines),
cmpint);
int j, c;
for (j = 0; lines[j]; j++) {
printf(" %d", *(int *)lines[j]);
c = 0;
while (lines[j+1]
&& *(int *)lines[j+1] == *(int *)lines[j] + 1) {
j++;
c = 1;
}
if (c)
printf("-%d", *(int *)lines[j]);
}
FREE(lines);
}
printf("\n");
}
FREE(array);
}
int main(int argc, char *argv[]) {
int i;
Table_T identifiers = Table_new(10000, textcmp, texthash);
Text_save_T mark = Text_save();
Fmt_register('T', Text_fmt);
Fmt_register('D', Integer_fmt);
first = Text_cat(Text_cat(Text_ucase, Text_lcase), Text_box("_", 1));
rest = Text_cat(first, Text_digits);
for (i = 1; i < argc; i++) {
FILE *fp = fopen(argv[i], "r");
if (fp == NULL)
fprintf(stderr, "%s: can't open '%s' (%s)\n", argv[0], argv[i], strerror(errno));
else {
cref(argv[i], fp, identifiers);
fclose(fp);
}
}
if (argc == 1)
cref(NULL, stdin, identifiers);
{
int i;
void **array = Table_toArray(identifiers, NULL);
qsort(array, Table_length(identifiers), 2*sizeof (*array), compare);
for (i = 0; array[i]; i += 2) {
Fmt_print("%T", array[i]);
print(array[i+1]);
FREE(array[i]);
}
FREE(array);
Table_free(&identifiers);
}
Text_restore(&mark);
return EXIT_SUCCESS;
}
void wf(char *name, FILE *fp) {
Table_T table = Table_new(0, NULL, NULL);
char buf[128];
while (getword(fp, buf, sizeof buf, first, rest)) {
const char *word;
int i, *count;
for (i = 0; buf[i] != '\0'; i++)
buf[i] = tolower(buf[i]);
word = Atom_string(buf);
count = Table_get(table, word);
if (count)
(*count)++;
else {
NEW(count);
*count = 1;
Table_put(table, word, count);
}
}
if (name)
printf("%s:\n", name);
{ int i;
void **array = Table_toArray(table, NULL);
qsort(array, Table_length(table), 2*sizeof (*array),
compare);
for (i = 0; array[i]; i += 2)
printf("%d\t%s\n", *(int *)array[i+1],
(char *)array[i]);
FREE(array); }
Table_map(table, vfree, NULL);
Table_free(&table);
}
void print(Table_T files){
int i;
void **array = Table_toArray(files, NULL);
qsort(array, Table_length(files), 2 * sizeof(*array), compare);
for (i = 0; array[i]; i += 2){
if (*(char *)array[i] != '\0'){
printf("\t%s:", (char *)array[i]);
}
// print the line numbers in the set array[i+1]
{
int j;
void **lines = Set_toArray(array[i + 1], NULL);
qsort(lines, Set_length(array[i+1], sizeof(*lines), cmpint);
for (j = 0; lines[j]; j++){
printf(" %d", *(int *)lines[j]);
}
FREE(lines);
}
printf("\n");
}
FREE(array);
}
int main(int argc, char *argv[]) {
int i;
Table_T identifiers = Table_new(5000,
(int (*)(const void *, const void *))strcmp, strhash);
Fmt_register('S', Str_fmt);
first = Str_catv("abcdefghijklmnopqrstuvwxyz", 1, 0,
"ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 0, "_", 1, 0, NULL);
rest = Str_cat(first, 1, 0, "0123456789", 1, 0);
for (i = 1; i < argc; i++) {
FILE *fp = fopen(argv[i], "r");
if (fp == NULL)
fprintf(stderr, "%s: can't open '%s' (%s)\n", argv[0], argv[i], strerror(errno));
else {
kref(argv[i], fp, identifiers);
fclose(fp);
}
}
if (argc == 1)
kref(NULL, stdin, identifiers);
{
int i;
void **array = Table_toArray(identifiers, NULL);
qsort(array, Table_length(identifiers), 2*sizeof (*array), compare);
for (i = 0; array[i]; i += 2) {
Fmt_print("%S", array[i], 1, 0);
print(array[i+1]);
FREE(array[i]);
}
FREE(array);
Table_free(&identifiers);
}
return EXIT_SUCCESS;
}
static void _cleanup(OeSession session) {
T _this_ = OeNet_get_proto(OeSession_get_net(session));
int sz = Table_length(_this_->pending);
void **array = Table_toArray(_this_->pending, NULL);
for ( int i = 0; i < sz && array[i]; i+= 2 ) {
CID_KEY *key = (CID_KEY *) array[i];
ACContext *pc = Table_remove(_this_->pending, key);
_send_con_closed(pc->context);
}
Mem_free(array, __FILE__, __LINE__);
Table_free(&_this_->pending);
//OepClient_free(&_this_); //closing the proto is hard and buggy.
}
/*finds and returns the number of sets with more than one value*/
int num_fgroups(Table_T* table)
{
int table_len = Table_length(*table);
void **table_array = Table_toArray(*table, NULL);
int counter = 0;
for (int i=1; i<(2*table_len); i += 2) {
if (Set_length((Set_T)table_array[i]) > 1) {
counter++;
}
}
free(table_array);
return counter;
}
static void _free_items(Table_T items) {
assert(items);
int sz = Table_length(items);
if (sz > 0) {
void **array = Table_toArray(items, NULL);
for ( int i = 0; i < sz && array[i]; i+= 2 ) {
char *key = (char *) array[i];
Set_T titem = Table_remove(items, key);
if (titem) {
Set_free( &titem );
}
}
Mem_free(array, __FILE__, __LINE__);
}
}
END_TEST
START_TEST(test_put_replace)
{
/* New values replace old values with the same key. */
Table_T *table = Table_new(0, cmpatom, hashatom);
Table_put(table, (void*)0x12, (void*)0x34);
Table_put(table, (void*)0x12, (void*)0x56);
fail_unless( Table_length(table) == 1 );
fail_unless( Table_get(table, (void*)0x12) == (void*)0x56);
Table_remove(table, (void*)0x12);
Table_free(&table);
}
/* prints the sets in the table that have more than 1 value*/
void print_table(Table_T* table)
{
int table_len = Table_length(*table);
void **table_array = Table_toArray(*table, NULL);
int counter = num_fgroups(table);
for (int i=1; i<(2*table_len); i += 2) {
if(Set_length((Set_T)table_array[i]) > 1) {
print_set((Set_T *)&table_array[i]);
counter--;
if (counter != 0) {
printf("\n");
}
}
Set_free((Set_T *)&table_array[i]);
}
free(table_array);
}
void print(Table_T files) {
int i;
void **array = Table_toArray(files, NULL);
qsort(array, Table_length(files), 2*sizeof (*array), compare);
for (i = 0; array[i]; i += 2) {
Seq_T seq = array[i+1];
char *filename = array[i];
if (*filename)
Fmt_print("\t%S:", filename, 1, 0);
while (Seq_length(seq) > 0)
Fmt_print(" %S", Seq_remhi(seq), 1, 0);
Fmt_print("\n");
FREE(filename);
Seq_free(&seq);
}
FREE(array);
Table_free(&files);
}
END_TEST
START_TEST(test_get)
{
/* Table_get() with non-existant key returns NULL */
Table_T *table = Table_new(0, cmpatom, hashatom);
Table_put(table, (void*)0x12, (void*)0x34);
fail_unless( Table_length(table) == 1 );
fail_unless( Table_get(table, (void*)0x12) == (void*)0x34);
/* non-existant key */
fail_unless( Table_get(table, (void*)0x34) == NULL);
Table_remove(table, (void*)0x12);
Table_free(&table);
}
void print_fgroups(T* table)
{
char ** arr = (char **)Table_toArray(*table, NULL);
int table_length = Table_length(*table) * 2;
for (int i=0; i < table_length; i+=2) {
L list_ptr = ((L)arr[i+1]);
int list_size = List_length(list_ptr);
if (list_size >= 2) {
char **names = (char**) List_toArray(list_ptr, NULL);
for (int j = 0; names[j]; j++)
printf("%s\n", (char*)(names[j]));
if (2*i+2 < table_length)
printf("\n");
free(names);
}
List_free(&list_ptr);
}
free(arr);
Table_free(table);
}
int try_running_tests_in_dso(struct herc *h, const char *file, void *handle) {
size_t i = 0;
void *suite_fixture, *test_fixture;
//get the suites
Table_T suitesTable = get_testnames_in_file(file, handle);
//convert to array for easier sorting and iteration
unsigned nSuites = Table_length(suitesTable);
void **suites = Table_toArray(suitesTable, 0);
Table_free(&suitesTable);
//sort
qsort(suites, nSuites, 2*sizeof(suites[0]), (int (*)(const void *, const void *))strcmp);
//iterate and run
for (i = 0; i<nSuites; i++) {
suite_desc *suite = suites[i*2+1];
suite_fixture = invoke_before_suite(suite);//TODO call RBE callback
cr_list_iter *iter = cr_list_iter_create(suite->tests);
while (!cr_list_iter_past_end(iter)) {
test_fixture = invoke_before_test(suite, suite_fixture);
test_desc *test = (test_desc*)cr_list_iter_get(iter);
herc_rbe_invoke(h->rbe, start_test, test);
run_test(h, handle, test, test_fixture);
herc_rbe_invoke(h->rbe, end_test, test);
invoke_after_test(suite, test_fixture);
cr_list_iter_next(iter);
}
cr_list_iter_free(iter);
invoke_after_suite(suite, suite_fixture);
}
for (i = 0; i<nSuites; i++) {
suite_desc_free(suites[i*2+1]);
}
free(suites);
return 0;
}
END_TEST
START_TEST(test_put_in_same_bucket)
{
/* Our hash function always places key/vals in the same bucket -
* assert that multiple items can be placed and retreived from
* the same bucket */
Table_T *table = Table_new(0, cmpatom, hashatom);
Table_put(table, (void*)0x12, (void*)0x34);
Table_put(table, (void*)0x56, (void*)0x78);
fail_unless( Table_length(table) == 2 );
fail_unless( Table_get(table, (void*)0x12) == (void*)0x34);
fail_unless( Table_get(table, (void*)0x56) == (void*)0x78);
Table_remove(table, (void*)0x12);
Table_remove(table, (void*)0x56);
Table_free(&table);
}
void print(Table_T files) {
int i;
void **array = Table_toArray(files, NULL);
qsort(array, Table_length(files), 2*sizeof (*array), compare);
for (i = 0; array[i]; i += 2) {
Ring_T ring = array[i+1];
Text_T *filename = array[i];
if (filename->len > 0)
Fmt_print("\t%T:", filename);
while (Ring_length(ring) > 0) {
Integer_T line = Ring_remhi(ring);
Fmt_print(" %D", line);
FREE(line);
}
Fmt_print("\n");
FREE(filename);
Ring_free(&ring);
}
FREE(array);
Table_free(&files);
}
int exponent_table_length(exponent_table *E)
{
return Table_length(E->table);
}
int main()
{
FILE *fp = fopen("test.txt", "r");
int c = 0;
int i = 0;
char s[512];
Table_T our_table = Table_new(10, NULL, NULL);
char * name;
const char *fingerprint;
const char* temp;
while((c=fgetc(fp)) != ' ' && c != EOF) //Fingerprint section
{
s[i]= c;
i++;
}
s[i] = '\0';
//Here we have fingerprint in s
fingerprint = Atom_string(s);
temp = Atom_string(s);
i = 0;
while((c = getc(fp)) != '\n' && c != EOF)
{
s[i] = c;
i++;
}
s[i] = '\0';
//Here we have name in s
name = s;
Table_put(our_table, fingerprint, name);
while( c != EOF)
{
i = 0;
while((c = fgetc(fp)) != ' ' && c != EOF) // Fingerprint section
{
s[i] = c;
i++;
}
s[i] = '\0';
fingerprint = Atom_string(s);
i = 0;
while((c = getc(fp)) != '\n' && c != EOF)
{
s[i] = c;
i++;
}
s[i] = '\0';
name = s;
printf("FP: %s\n ", fingerprint);
printf("NAME: %s\n", name);
char * test = Table_put(our_table, fingerprint, name);
printf("idk: %s\n", test);
// printf("VALUE STORED IN FP: %s\n\n", (char *)Table_get(our_table, temp));
}
// NEED TO DEAL WITH TABLE MAP AND IMPLEMENTING A LIST
// Table_map(our_table, vfree, NULL);
//printf("%s", fingerprint);
// printf("%s", (char *)Table_get(our_table, fingerprint));
printf("%d", Table_length(our_table));
// Table_map(our_table, vfree, NULL);
int length = Table_length(our_table);
void **table = Table_toArray(our_table, NULL);
for(int x = 0; x < 2*length; x++)
{
printf("%s ", (char *)table[x]);
}
Table_free(&our_table);
return 0;
}
static void
write_contig_file (char *genomesubdir, char *fileroot, Table_T accsegmentpos_table,
Tableint_T chrlength_table, List_T contigtypelist) {
FILE *textfp;
char *textfile, *iitfile, *annot;
int naccessions, i;
char **accessions, *divstring;
Segmentpos_T segmentpos;
Chrom_T chrom;
Genomicpos_T chroffset, universalpos1, universalpos2;
List_T divlist = NULL, intervallist = NULL, labellist = NULL, annotlist = NULL, p;
Table_T intervaltable, labeltable, annottable;
Interval_T interval;
#if 0
void **keys;
int *values, ntypes;
#endif
if (divsort == NO_SORT) {
accessions = (char **) Table_keys_by_timeindex(accsegmentpos_table,NULL);
naccessions = Table_length(accsegmentpos_table);
} else {
/* Get accessions in order */
accessions = (char **) Table_keys(accsegmentpos_table,NULL);
naccessions = Table_length(accsegmentpos_table);
current_accsegmentpos_table = accsegmentpos_table;
qsort(accessions,naccessions,sizeof(char *),bysegmentpos_compare);
}
#if 0
/* Get types in order */
keys = Tableint_keys(contigtype_table,NULL);
values = Tableint_values(contigtype_table,0);
ntypes = Tableint_length(contigtype_table);
contigtypes = (char **) CALLOC(ntypes+1,sizeof(char *)); /* Add 1 for type 0 */
contigtypes[0] = "";
for (j = 0; j < ntypes; j++) {
contigtypes[values[j]] = keys[j];
}
FREE(values);
FREE(keys);
#endif
/* Write contig text file */
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".contig")+1,sizeof(char));
sprintf(textfile,"%s/%s.contig",genomesubdir,fileroot);
/* Use binary, not text, so files are Unix-compatible */
if ((textfp = FOPEN_WRITE_BINARY(textfile)) == NULL) {
fprintf(stderr,"Can't write to file %s\n",textfile);
exit(9);
}
FREE(textfile);
for (i = 0; i < naccessions; i++) {
segmentpos = (Segmentpos_T) Table_get(accsegmentpos_table,(void *) accessions[i]);
chrom = Segmentpos_chrom(segmentpos);
chroffset = (Genomicpos_T) Tableint_get(chrlength_table,chrom);
universalpos1 = chroffset + Segmentpos_chrpos1(segmentpos);
universalpos2 = chroffset + Segmentpos_chrpos2(segmentpos);
/* Print as 1-based, inclusive [a,b] */
if (Segmentpos_revcompp(segmentpos) == true) {
fprintf(textfp,"%s\t%u..%u\t%s:%u..%u\t%u",
accessions[i],universalpos2+1U,universalpos1,
Chrom_string(chrom),Segmentpos_chrpos2(segmentpos)+1U,Segmentpos_chrpos1(segmentpos),
Segmentpos_length(segmentpos));
} else {
fprintf(textfp,"%s\t%u..%u\t%s:%u..%u\t%u",
accessions[i],universalpos1+1U,universalpos2,
Chrom_string(chrom),Segmentpos_chrpos1(segmentpos)+1U,Segmentpos_chrpos2(segmentpos),
Segmentpos_length(segmentpos));
}
#if 0
if (Segmentpos_type(segmentpos) > 0) {
fprintf(textfp,"\t%s",contigtypes[Segmentpos_type(segmentpos)]);
}
#endif
fprintf(textfp,"\n");
/* Store as 0-based, inclusive [a,b] */
labellist = List_push(labellist,(void *) accessions[i]);
if (Segmentpos_revcompp(segmentpos) == true) {
/* The negative sign in the interval is the indication that the
contig was reverse complement */
intervallist = List_push(intervallist,
(void *) Interval_new(universalpos2-1U,universalpos1,
Segmentpos_type(segmentpos)));
} else {
intervallist = List_push(intervallist,
(void *) Interval_new(universalpos1,universalpos2-1U,
Segmentpos_type(segmentpos)));
}
#if 0
/* IIT version 1 */
sprintf(seglength,"%u",Segmentpos_length(segmentpos));
annot = (char *) CALLOC(strlen(seglength)+1,sizeof(char));
strcpy(annot,seglength);
#else
/* IIT versions >= 2 */
annot = (char *) CALLOC(1,sizeof(char));
annot[0] = '\0';
#endif
annotlist = List_push(annotlist,(void *) annot);
}
fclose(textfp);
#if 0
FREE(contigtypes);
#endif
FREE(accessions);
intervallist = List_reverse(intervallist);
/* contigtypelist = List_reverse(contigtypelist); -- Done by caller */
labellist = List_reverse(labellist);
annotlist = List_reverse(annotlist);
/* Write contig IIT file */
divstring = (char *) CALLOC(1,sizeof(char));
divstring[0] = '\0';
divlist = List_push(NULL,divstring);
intervaltable = Table_new(65522,Table_string_compare,Table_string_hash);
labeltable = Table_new(65522,Table_string_compare,Table_string_hash);
annottable = Table_new(65522,Table_string_compare,Table_string_hash);
Table_put(intervaltable,(void *) divstring,intervallist);
Table_put(labeltable,(void *) divstring,labellist);
Table_put(annottable,(void *) divstring,annotlist);
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.contig.iit",genomesubdir,fileroot);
#if 0
debug(
for (p = contigtypelist; p != NULL; p = List_next(p)) {
printf("Type %s\n",(char *) List_head(p));
}
);
