}
catch(exception& e) {
- errorOut(e, "KmerDB", "KmerDB");
+ m->errorOut(e, "KmerDB", "KmerDB");
exit(1);
}
}
/**************************************************************************************************/
+KmerDB::KmerDB() : Database() {}
+/**************************************************************************************************/
KmerDB::~KmerDB(){}
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);
+ 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
- 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);
+ //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) {
- errorOut(e, "KmerDB", "findClosestSequences");
+ m->errorOut(e, "KmerDB", "findClosestSequences");
exit(1);
}
}
try {
ofstream kmerFile; // once we have the kmerLocations folder print it out
- openOutputFile(kmerDBName, kmerFile); // to a file
+ m->openOutputFile(kmerDBName, kmerFile); // to a file
+
+ //output version
+ 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
}
catch(exception& e) {
- errorOut(e, "KmerDB", "generateDB");
+ m->errorOut(e, "KmerDB", "generateDB");
exit(1);
}
count++;
}
catch(exception& e) {
- errorOut(e, "KmerDB", "addSequence");
+ m->errorOut(e, "KmerDB", "addSequence");
exit(1);
}
}
kmerDBFile.seekg(0); // start at the beginning of the file
+ //read version
+ string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
+
string seqName;
int seqNumber;
}
catch(exception& e) {
- errorOut(e, "KmerDB", "readKmerDB");
+ m->errorOut(e, "KmerDB", "readKmerDB");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+int KmerDB::getCount(int kmer) {
+ try {
+ if (kmer < 0) { return 0; } //if user gives negative number
+ else if (kmer > maxKmer) { return 0; } //or a kmer that is bigger than maxkmer
+ else { return kmerLocations[kmer].size(); } // kmer is in vector range
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getCount");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<int> KmerDB::getSequencesWithKmer(int kmer) {
+ try {
+
+ vector<int> seqs;
+
+ if (kmer < 0) { } //if user gives negative number
+ else if (kmer > maxKmer) { } //or a kmer that is bigger than maxkmer
+ else { seqs = kmerLocations[kmer]; }
+
+ return seqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getSequencesWithKmer");
exit(1);
}
}
+/**************************************************************************************************/
+
/**************************************************************************************************/
+
+