void
AntiDOS_update(AntiDOS *dos)
{
time_t t = time(0);
assert(dos!=0);
if (t-dos->min_time > ANTIDOS_TIME_BASE) {
bool was_changed = false;
struct Data *i;
dos->min_time = t;
for (i = Vector_begin(&dos->data); i!=Vector_end(&dos->data); ++i) {
if (t - i->access_time>ANTIDOS_TIME_BASE) {
i->ip.s_addr = 0xFFFFFFFF;
was_changed = true;
}
else
dos->min_time = MIN(dos->min_time, i->access_time);
}
if (was_changed) {
Vector_sort(&dos->data, Data_sortCompare);
for (i=Vector_end(&dos->data); i!=Vector_begin(&dos->data);) {
--i;
if (i->ip.s_addr!=0xFFFFFFFF) break;
Vector_popback(&dos->data);
}
Vector_resize(&dos->data);
}
}
}
char *Translation_modifyTranslation(Translation *translation, char *seq) {
Vector *seqEds = Translation_getAllSeqEdits(translation);
// Sort in reverse order to avoid complication of adjusting
// downstream edits.
// HACK: The translation ENSP00000420939 somehow makes the next line
// bomb out ($a or $b becomes undef) if the start() method
// is used. I haven't been able to find out why. It has 10
// Selenocysteine seqedits that looks correct.
// /Andreas (release 59)
if (Vector_getNumElement(seqEds)) {
Vector_sort(seqEds, SeqEdit_reverseStartCompFunc);
// @seqeds = sort { $b->{'start'} <=> $a->{'start'} } @seqeds;
// Apply all edits.
// Not particularly efficient currently, could improve by precalculating maximum size of new seq prior to applying edits
int i;
for (i=0; i<Vector_getNumElement(seqEds); i++) {
SeqEdit *se = Vector_getElementAt(seqEds, i);
seq = SeqEdit_applyEdit(se, seq);
}
//$seq->seq($peptide);
}
Vector_free(seqEds);
return seq;
}
Vector *getGenes(Slice *slice, int flags) {
Vector *genes;
genes = Slice_getAllGenes(slice, NULL, NULL, 1, NULL, NULL);
Vector_sort(genes, geneStartCompFunc);
return genes;
}
void PredictionTranscript_sort(PredictionTranscript *trans) {
PredictionExon *firstExon = PredictionTranscript_getExonAt(trans,0);
int strand;
int i;
for (i=0; i<PredictionTranscript_getExonCount(trans); i++) {
if (!PredictionTranscript_getExonAt(trans,i)) {
return;
}
}
strand = PredictionExon_getStrand(firstExon);
// Hack in using Exon function names
if (strand == 1) {
Vector_sort(PredictionTranscript_getExons(trans),Exon_forwardStrandCompFunc);
} else if (strand == -1) {
Vector_sort(PredictionTranscript_getExons(trans),Exon_reverseStrandCompFunc);
}
}
Vector *GenomicAlignAdaptor_mergeAlignsets(GenomicAlignAdaptor *gaa, Vector *alignSet1, Vector *alignSet2) {
int i;
Vector *bigList = Vector_new();
IDHash *overlappingSets[2];
Vector *mergedAligns;
for (i=0;i<Vector_getNumElement(alignSet1); i++) {
GenomicAlign *align = Vector_getElementAt(alignSet1, i);
Vector_addElement(bigList, GenomicAlignListElem_new(DNAFrag_getDbID(GenomicAlign_getQueryDNAFrag(align)),
GenomicAlign_getQueryStart(align), align, 0));
Vector_addElement(bigList, GenomicAlignListElem_new(DNAFrag_getDbID(GenomicAlign_getQueryDNAFrag(align)),
GenomicAlign_getQueryEnd(align)+0.5, align, 0));
}
for (i=0;i<Vector_getNumElement(alignSet2); i++) {
GenomicAlign *align = Vector_getElementAt(alignSet2, i);
Vector_addElement(bigList, GenomicAlignListElem_new(DNAFrag_getDbID(GenomicAlign_getConsensusDNAFrag(align)),
GenomicAlign_getConsensusStart(align), align, 1));
Vector_addElement(bigList, GenomicAlignListElem_new(DNAFrag_getDbID(GenomicAlign_getConsensusDNAFrag(align)),
GenomicAlign_getConsensusEnd(align)+0.5, align, 1));
}
Vector_sort(bigList, GenomicAlignListElem_compFunc);
// walking from start to end through sortlist and keep track of the
// currently overlapping set of Alignments
overlappingSets[0] = IDHash_new(IDHASH_SMALL);
overlappingSets[1] = IDHash_new(IDHASH_SMALL);
mergedAligns = Vector_new();
for (i=0; i<Vector_getNumElement(bigList); i++) {
GenomicAlignListElem *gale = Vector_getElementAt(bigList,i);
GenomicAlign *align = gale->align;
IDType alignID = GenomicAlign_getDbID(align);
int setNo = gale->setNum;
if (IDHash_contains(overlappingSets[setNo], alignID)) {
// remove from current overlapping set
IDHash_remove(overlappingSets[setNo], alignID, NULL);
} else {
int j;
void **values = IDHash_getValues(overlappingSets[1-setNo]);
// insert into the set and do all the overlap business
IDHash_add(overlappingSets[setNo], alignID, align);
// the other set contains everything this align overlaps with
for (j=0; j<IDHash_getNumValues(overlappingSets[1-setNo]); j++) {
GenomicAlign *align2 = values[j];
if (setNo == 0) {
GenomicAlignAdaptor_addDerivedAlignments(gaa, mergedAligns, align, align2);
} else {
GenomicAlignAdaptor_addDerivedAlignments(gaa, mergedAligns, align2, align);
}
}
free(values);
}
}
// NIY Free gale
return mergedAligns;
}
