void difference_clip(GapIO *io, int num_contigs, contig_list_t *cl,
int add_tags)
{
int i, nbases;
int *old_start, *old_end;
int all;
if (NULL == (old_start = (int *)xcalloc(NumReadings(io)+1, sizeof(int))))
return;
if (NULL == (old_end = (int *)xcalloc(NumReadings(io)+1, sizeof(int))))
return;
for (i = 0; i < num_contigs; i++) {
vmessage("--Contig %s--\n", io_rname(io, io_clnbr(io, cl[i].contig)));
all = (cl[i].start == 1 && cl[i].end == io_clength(io, cl[i].contig))
? 1 : 0;
nbases = difference_clip_contig(io, cl[i].contig, cl[i].start,
cl[i].end, old_start, old_end,
add_tags);
/*
* if (all)
* nbases += quality_clip_ends(io, cl[i].contig, add_tags);
*/
vmessage(" Clipped %d bases\n", nbases);
reorder_readings(io, cl[i].contig);
fix_holes(io, cl[i].contig, old_start, old_end);
reorder_readings(io, cl[i].contig);
flush2t(io);
vmessage("\n");
}
xfree(old_start);
xfree(old_end);
}
void ed_nip_renz_info(int seq_num,
ed_renz_res *data,
int start,
int print_opt)
{
int seq_len;
char *seq;
int sequence_type;
seq = GetEdenSeq(seq_num);
seq_len = GetEdenLength(seq_num);
/*sequence_type = GetSequenceStructure(seq_num);*/
sequence_type = GetEdenType(seq_num);
vfuncheader("Restriction enzymes result list");
vmessage("Sequence %s\n", GetEdenName(seq_num));
vmessage("Number of enzymes = %d\n", data->num_enzymes);
vmessage("Number of matches = %d\n", data->num_match);
if (print_opt == 0) {
start_message();
EdPrintEnzymeByEnzyme(data->r_enzyme, data->match, data->num_match,
data->num_enzymes, seq, seq_len,
sequence_type, start);
end_message(data->re_win);
} else {
start_message();
EdOrderOnPosition(data->r_enzyme, data->match, data->num_match,
seq, seq_len, sequence_type, start);
end_message(data->re_win);
}
}
/*
* Removes some or all tags from some or all contigs.
* If the contig list or tag list is blank it implies all contigs or all tags.
*
* Returns 0 on success
* -1 on failure
*/
int delete_tags(GapIO *io, int ncontigs, contig_list_t *contigs,
char *tag_list, int verbose) {
HashTable *h = NULL;
int ret = 0;
/* Hash tag types */
if (tag_list && *tag_list) {
int i;
if (SetActiveTags(tag_list) == -1) {
return -1;
}
h = HashTableCreate(32, 0);
for (i = 0; i < number_of_active_tags; i++) {
HashData hd;
hd.i = 0;
HashTableAdd(h, active_tag_types[i], 4, hd, NULL);
}
}
/* Iterate over contig list or all contigs */
if (verbose)
vfuncheader("Delete Tags");
if (ncontigs) {
int i;
for (i = 0; i < ncontigs; i++) {
contig_t *c = cache_search(io, GT_Contig, contigs[i].contig);
vmessage("Scanning contig %d of %d (%s)\n",
i+1, ncontigs, c->name);
ret |= delete_tag_single_contig(io, contigs[i].contig, h, verbose);
UpdateTextOutput();
cache_flush(io);
}
} else {
int i;
tg_rec *order = ArrayBase(tg_rec, io->contig_order);
for (i = 0; i < NumContigs(io); i++) {
contig_t *c = cache_search(io, GT_Contig, order[i]);
vmessage("Scanning contig %d of %d (%s)\n",
i+1, NumContigs(io), c->name);
ret |= delete_tag_single_contig(io, order[i], h, verbose);
UpdateTextOutput();
cache_flush(io);
}
}
SetActiveTags("");
if (h)
HashTableDestroy(h, 0);
return ret;
}
int shuffle_contigs_io(GapIO *io, int ncontigs, contig_list_t *contigs,
int band) {
int i;
set_malign_lookup(5);
/* set_alignment_matrix("/tmp/nuc_matrix", "ACGTURYMWSKDHVB-*"); */
for (i = 0; i < ncontigs; i++) {
int cnum = contigs[i].contig;
int old_score, new_score, tot_score, orig_score;
MALIGN *malign = build_malign(io, cnum);
vmessage("Shuffling pads for contig %s\n", get_contig_name(io, cnum));
/* print_malign(malign); */
orig_score = new_score = malign_diffs(malign, &tot_score);
vmessage("Initial score %.2f%% mismatches (%d mismatches)\n",
(100.0 * orig_score)/tot_score, orig_score);
UpdateTextOutput();
do {
old_score = new_score;
malign = realign_seqs(cnum, malign, band);
/* print_malign(malign); */
new_score = malign_diffs(malign, &tot_score);
vmessage(" Number of differences to consensus: %d\n", new_score);
UpdateTextOutput();
} while (new_score < old_score);
if (new_score < orig_score) {
update_io(io, cnum, malign);
} else {
vmessage("Could not reduce number of consensus differences.\n");
}
destroy_malign(malign, 1);
vmessage("Final score %.2f%% mismatches\n",
(100.0 * new_score)/tot_score);
/*
* Sequences like
* AGCT**GATGC
* TGGATCGA
* can end up causing holes. We break the contig in this case to
* avoid minor database inconsistencies.
*/
remove_contig_holes(io, cnum);
/* reassign_confidence_values(io, cnum); */
}
flush2t(io);
return 0;
}
/*
* Wrapper around find_oligos() to look for all oligos listed in a FASTA file.
*/
int
find_oligo_file(GapIO *io,
int num_contigs,
contig_list_t *contig_array,
float mis_match,
char *file,
int consensus_only,
int in_cutoff)
{
char **ids;
int nids;
int i;
int r = 0; /* ret. code */
/* Use seq_utils to parse the input file */
if (0 != get_identifiers(file, &ids, &nids))
return -1;
for (i = 0; i < nids; i++) {
char *seq;
int seq_len;
seq = NULL;
seq_len = 0;
if (0 != get_seq(&seq, maxseq, &seq_len, file, ids[i]))
continue;
if (seq_len == 0 || !seq || *seq == 0) {
if (seq)
xfree(seq);
continue;
}
vmessage("Sequence search for ID '%s'\n", ids[i]);
r |= find_oligos(io, num_contigs, contig_array, mis_match,
seq, consensus_only, in_cutoff);
vmessage("\n");
if (seq)
xfree(seq);
}
/* Tidy up memory */
for (i = 0; i < nids; i++) {
xfree(ids[i]);
}
xfree(ids);
return r;
}
/*
* Provide information about a set of matches - the meta object.
*/
void csmatch_info(mobj_repeat *r, char *name) {
int i;
vfuncheader("%s result list", name);
vmessage("Number of matches = %d\n", r->num_match);
vmessage("Display colour = %s\n", r->colour);
for (i = 0; i < r->num_match; i++) {
obj_match *obj = &r->match[i];
int op = -1; /* For match operations, -1 is always "Information" */
vmessage("\nMatch %d:\n", i);
obj->func(OBJ_INVOKE_OPERATION, &op, obj, obj->data);
}
}
void info(const char* fmt, ...){
va_list ap;
va_start(ap, fmt);
vmessage(Log_Info, fmt, ap);
va_end(ap);
}
void warning(const char* fmt, ...){
va_list ap;
va_start(ap, fmt);
vmessage(Log_Warning, fmt, ap);
va_end(ap);
}
void fatal(const char* fmt, ...){
va_list ap;
va_start(ap, fmt);
vmessage(Log_Fatal, fmt, ap);
va_end(ap);
}
void verbose(const char* fmt, ...){
va_list ap;
va_start(ap, fmt);
vmessage(Log_Verbose, fmt, ap);
va_end(ap);
}
OfxStatus setPersistentMessage(const char* type,
const char* id,
const char* format,
va_list args)
{
return vmessage(type, id, format, args);
}
void closeUndo(EdStruct *xx, DBInfo *db)
/*
* Start recording undo for next command
*/
{
if (--_DBI_open_undo_count(db) != 0)
return;
if (!_DBI_store_undo(db))
return;
if (_DBI_num_undo(db) > 0 &&
_DBI_undo_lists(db)[_DBI_last_undo(db)] == NULL){
_DBI_last_undo(db) = (_DBI_last_undo(db) + MAX_SAVE_EDITS - 1) %
MAX_SAVE_EDITS;
_DBI_num_undo(db)--;
if (--_DBI_edits_made(db) < 0) {
_DBI_edits_made(db) = 0;
}
}
if (xx->auto_save && _DBI_edits_made(db) >= AUTO_SAVE_EDITS) {
vmessage("Contig Editor: auto saving\n");
UpdateTextOutput();
saveDB(xx, _DBI_io(db), 1 /* an autosave */, 1 /* notify others */);
}
}
void notice(const char *format, ...)
{
va_list ap;
va_start(ap, format);
vmessage(LOG_NOTICE, format, ap);
va_end(ap);
}
void error(const char *format, ...)
{
va_list ap;
va_start(ap, format);
vmessage(LOG_ERR, format, ap);
va_end(ap);
}
void message(int loglevel, const char *format, ...)
{
va_list ap;
va_start(ap, format);
vmessage(loglevel, format, ap);
va_end(ap);
}
/* PRINTFLIKE1 */
void
warn(const char *fmt, ...)
{
va_list va;
va_start(va, fmt);
vmessage(fmt, va);
va_end(va);
}
void error(const char *msg, ...)
{
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
va_list ap;
va_start(ap, msg);
vmessage(stderr, msg, "error:", RED, ap);
va_end(ap);
}
void warning(const char *msg, ...)
{
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
va_list ap;
va_start(ap, msg);
vmessage(stderr, msg, "warning:", YELLOW, ap);
va_end(ap);
}
void debug(const char *format, ...)
{
va_list ap;
if (!verbose_mode)
return;
va_start(ap, format);
vmessage(LOG_DEBUG, format, ap);
va_end(ap);
}
int write_screen_genetic_code (char code_table[5][5][5] ) {
/* write out a genetic code table */
int i,k;
char bases[] = {"tcag-"};
for(i = 0; i < 4; i++) {
vmessage(" ===============================================\n");
for(k = 0; k < 4; k++) {
vmessage(" %c %c%c%-7c %c %c%c%-7c %c %c%c%-7c %c %c%c%-7c\n",
genetic_code[i][0][k],bases[i],bases[0],bases[k],
genetic_code[i][1][k],bases[i],bases[1],bases[k],
genetic_code[i][2][k],bases[i],bases[2],bases[k],
genetic_code[i][3][k],bases[i],bases[3],bases[k]);
}
}
vmessage(" ===============================================\n");
return 1;
}
void info(const char *msg, ...)
{
if (LOG_LEVEL < 1)
return;
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
va_list ap;
va_start(ap, msg);
vmessage(stdout, msg, "info:", BLUE, ap);
va_end(ap);
}
void debug(const char *msg, ...)
{
if (LOG_LEVEL < 2)
return;
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
va_list ap;
va_start(ap, msg);
vmessage(stdout, msg, "debug:", GREEN, ap);
va_end(ap);
}
/* PRINTFLIKE1 */
void
semerr(const char *fmt, ...)
{
va_list va;
va_start(va, fmt);
vmessage(fmt, va);
va_end(va);
if ((est->sc_cmd_flags & (SC_CMD_IACTIVE | SC_CMD_DONT_EXIT)) == 0)
exit(1);
}
int dofiles ( int a, char *v[] )
/* sets global PROGNAME, FILEIN, FILEOUT - must be called first */
{
FILEIN = NULL;
FILEOUT = NULL;
vmessage();
if (a > 3) a = 3;
switch (a) {
case 3: FILEOUT = v[2];
case 2: FILEIN = v[1];
case 1: PROGNAME = v[0]; }
return(0);
}
/* creates an empty header */
PICTURE *newpic(void)
{
PICTURE *pic;
vmessage();
pic = (PICTURE *)malloc(sizeof(PICTURE));
if (pic == NULL)
{
(void)fprintf(stderr,"newpic: failed to allocate memory\n");
return(NULL);
}
pic->data = pic->udata = pic->adata = NULL;
pic->magic = 0;
return(pic);
}
void nip_stop_codons_text_func(void *obj)
{
seq_result *s_result = (seq_result *) obj;
Tcl_Obj *graph_obj = s_result->data;
int i;
Graph *graph;
graph = Tcl_GetGraphFromObj(graph_obj);
for (i = 0; i < graph->d_arrays[0].n_dlines; i++) {
UpdateTextOutput();
vmessage("Position %10f\n", graph->d_arrays[0].d_array[i].x0);
}
}
void
splice_search_text_func(void *obj)
{
seq_result *result = (seq_result *) obj;
stick *data = result->data;
text_wtmatrix **text_data = result->text_data;
int i;
char *sequence;
int seq_num;
seq_num = GetSeqNum(result->seq_id[0]);
sequence = GetSeqSequence(seq_num);
vmessage("Donor\n");
for (i = 0; i < data->ap_array[0].n_pts; i++) {
UpdateTextOutput();
vmessage("Position %8d %8d score %f %.*s\n",
data->ap_array[0].p_array[i].pos - text_data[0]->mark_pos,
data->ap_array[0].p_array[i].pos + 1,
data->ap_array[0].p_array[i].score,
text_data[0]->length,
&sequence[data->ap_array[0].p_array[i].pos - 1 -
text_data[0]->mark_pos]);
}
vmessage("Acceptor\n");
for (i = 0; i < data->ap_array[1].n_pts; i++) {
UpdateTextOutput();
vmessage("Position %8d %8d score %f %.*s\n",
data->ap_array[1].p_array[i].pos - text_data[1]->mark_pos,
data->ap_array[1].p_array[i].pos + 1,
data->ap_array[1].p_array[i].score,
text_data[1]->length,
&sequence[data->ap_array[1].p_array[i].pos - 1 -
text_data[1]->mark_pos]);
}
}
int write_screen_cod_table (double codon_table[4][4][4] ) {
/* write out a codon table */
int i,k;
char bases[] = {"tcag"};
for(i = 0; i < 4; i++) {
vmessage(" ===============================================\n");
for(k=0;k<4;k++) {
vmessage(" %c %c%c%c%6.0f %c %c%c%c%6.0f %c %c%c%c%6.0f %c %c%c%c%6.0f\n",
genetic_code[i][0][k],bases[i],bases[0],bases[k],
codon_table[i][0][k],
genetic_code[i][1][k],bases[i],bases[1],bases[k],
codon_table[i][1][k],
genetic_code[i][2][k],bases[i],bases[2],bases[k],
codon_table[i][2][k],
genetic_code[i][3][k],bases[i],bases[3],bases[k],
codon_table[i][3][k]);
}
}
vmessage(" ===============================================\n");
return 1;
}
void fatal(const char* fmt, ...){
/*
* Make sure to get some output:
*/
if(output.empty()) {
add_destination(FATAL, stderr, false);
}
va_list ap;
va_start(ap, fmt);
vmessage(FATAL, fmt, ap);
va_end(ap);
fatal_func();
}
/*
* add a new sequence to sequence list
* add a new sequence to registration scheme
* update the sequence list box
* return the sequence number just created
*/
int AddSequence(Tcl_Interp *interp,
int direction,
int library,
char *entry,
char *sequence,
int seq_structure,
int seq_type,
Featcds **key_index,
char *identifier)
{
int seq_num;
#ifdef FIXME
/*
* don't do this yet - this ends up removing plots when I do translations
* twice. All needs careful thinking about!
*/
/* check if adding same sequence name, if are, remove previous seq */
RemoveDuplicateSeq(interp, entry);
#endif
seq_num = CheckSeqExists(entry, sequence);
if (seq_num > -1) {
xfree(sequence);
return seq_num;
}
/* add seq_num to seqs array */
seq_num = SeqCreate();
if (-1 == Set_Seqs(seq_num, direction, library, entry, sequence,
seq_structure, seq_type, key_index, identifier)) {
Delete_Seq(seq_num);
return -1;
}
/* add cur_seq_num to registration scheme */
if (-1 == add_reg_seq(seq_num)) {
Delete_Seq(seq_num);
return -1;
}
vmessage("Added sequence %s\n", entry);
return seq_num;
}
