inline void
onFindImpl(LocalDataHolder<TMatch, TGlobalHolder, TScoreExtension> & lH,
TSeedId const & seedId,
TSubjOcc subjOcc)
{
if (TGlobalHolder::indexIsFM) // positions are reversed
setSeqOffset(subjOcc,
length(lH.gH.subjSeqs[getSeqNo(subjOcc)])
- getSeqOffset(subjOcc)
- lH.options.seedLength);
Match m {static_cast<Match::TQId>(lH.seedRefs[seedId]),
static_cast<Match::TSId>(getSeqNo(subjOcc)),
static_cast<Match::TPos>(lH.seedRanks[seedId] * lH.options.seedOffset),
static_cast<Match::TPos>(getSeqOffset(subjOcc))};
bool discarded = false;
auto const halfSubjL = lH.options.seedLength / 2;
if (!sIsTranslated(lH.gH.blastProgram))
{
for (unsigned k = 0; k < length(lH.gH.segIntStarts[m.subjId]); ++k)
{
// more than half of the seed falls into masked interval
if (intervalOverlap(m.subjStart,
m.subjStart + lH.options.seedLength,
lH.gH.segIntStarts[m.subjId][k],
lH.gH.segIntEnds[m.subjId][k])
>= halfSubjL)
{
++lH.stats.hitsMasked;
discarded = true;
break;
}
}
}
if ((!discarded) && (!seedLooksPromising(lH, m)))
{
discarded = true;
++lH.stats.hitsFailedPreExtendTest;
}
if (!discarded)
lH.matches.emplace_back(m);
}
inline void
onFindDoubleIndex(LocalDataHolder<TMatch, TGlobalHolder, TScoreExtension> & lH,
TFinder const & finder)
{
auto qryOccs = getOccurrences(back(finder.patternStack));
auto subjOccs = getOccurrences(back(finder.textStack));
lH.stats.hitsAfterSeeding += length(qryOccs) * length(subjOccs);
for (unsigned i = 0; i < length(qryOccs); ++i)
for (unsigned j = 0; j < length(subjOccs); ++j)
onFindImpl(lH, getSeqNo(qryOccs[i]), subjOccs[j]);
}
//function checks if incoming packet is already in buffer
//verified
int checkSpace(int seq,char ** space,int *loc){
int k;
for(k=0;k<5;k++){
if(loc[k]==0){
continue;
}
if( seq == getSeqNo(space[k],1)){
return 1;
}
}
return 0;
}
//establishes by waiting for SYN packet from sender. Returns SENDER seq #
//verified
int estConn( struct sockaddr_in *cli_addr,int sockfd,struct Info *c,char * dip, char * dpt){
//printf("Waiting for sender....\n");
char buffer[MAXBUFLEN];
socklen_t cli_len = sizeof(*cli_addr);
int verify = recvfrom(sockfd, buffer, MAXBUFLEN-1 , 0,(struct sockaddr *)&*cli_addr, &cli_len);
if(verify==-1){
printf("error on recvfrom()\nExit..\n");
exit(1);
}
buffer[verify] = '\0';
int type = isA(buffer);
if(type == 1){ //got syn
printEvent(2,2,buffer,"SYN",dip,dpt);
c->syn_rcv+=1;
c->total_bytes_rcv+=strlen(buffer);
c->unique_bytes_rcv+=strlen(buffer);
c->total_packets_rcv+=1;
c->unique_packets_rcv+=1;
}
else{
return -1;
}
int s_seq = getSeqNo(buffer,1) + strlen(buffer);
char * tosend = makePack(s_seq,1);
//printf("tosend:\n%s\n",tosend);
int charsent;
if ((charsent = sendto(sockfd, tosend, strlen(tosend), 0,(struct sockaddr *)&*cli_addr, cli_len) == -1)) {
perror("sws: error in sendto()");
exit(1);
}
printEvent(1,2,tosend,"ACK",dip,dpt);
c->ack_sent+=1;
free(tosend);
return s_seq;
}
