vector<int> topMatches;
Kmer kmer(kmerSize);
searchScore = 0;
+ Scores.clear();
vector<int> matches(numSeqs, 0); // a record of the sequences with shared kmers
vector<int> timesKmerFound(kmerLocations.size()+1, 0); // a record of the kmers that we have already found
}
timesKmerFound[kmerNumber] = 1; // ok, we've seen the kmer now
}
-
- vector<seqMatch> seqMatches;
- for(int i=0;i<numSeqs;i++){
- seqMatch temp(i, matches[i]);
- seqMatches.push_back(temp);
- }
-
- //sorts putting largest matches first
- sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
- searchScore = seqMatches[0].match;
- searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
-
- //save top matches
- for (int i = 0; i < num; i++) {
- topMatches.push_back(seqMatches[i].seq);
+ if (num != 1) {
+ vector<seqMatch> seqMatches; seqMatches.resize(numSeqs);
+ for(int i=0;i<numSeqs;i++){
+ seqMatches[i].seq = i;
+ seqMatches[i].match = matches[i];
+ }
+
+ //sorts putting largest matches first
+ sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
+
+ searchScore = seqMatches[0].match;
+ searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
+
+ //save top matches
+ for (int i = 0; i < num; i++) {
+ topMatches.push_back(seqMatches[i].seq);
+ float thisScore = 100 * seqMatches[i].match / (float) numKmers;
+ Scores.push_back(thisScore);
+ }
+ }else{
+ int bestIndex = 0;
+ int bestMatch = -1;
+ for(int i=0;i<numSeqs;i++){
+
+ if (matches[i] > bestMatch) {
+ bestIndex = i;
+ bestMatch = matches[i];
+ }
+ }
+
+ searchScore = bestMatch;
+ searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
+ topMatches.push_back(bestIndex);
+ Scores.push_back(searchScore);
}
-
return topMatches;
}
catch(exception& e) {
m->openOutputFile(kmerDBName, kmerFile); // to a file
//output version
- kmerFile << m->getVersion() << endl;
+ kmerFile << "#" << m->getVersion() << endl;
for(int i=0;i<maxKmer;i++){ // step through all of the possible kmer numbers
kmerFile << i << ' ' << kmerLocations[i].size(); // print the kmer number and the number of sequences with