fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / kmerdb.cpp

diff --git a/kmerdb.cpp b/kmerdb.cpp
index bd5b9762b41dbc63e116172ad00e419755fdbbf1..e7e8ab2acbbf04c8bc30c6adb84fbd3880f7b2d8 100644 (file)
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -75,24 +75,39 @@ vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
                        }
                        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);
+                       }
+               }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);
                }
-               
                return topMatches;              
        }
        catch(exception& e) {
@@ -107,10 +122,10 @@ void KmerDB::generateDB(){
        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;
+               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
@@ -160,7 +175,7 @@ void KmerDB::readKmerDB(ifstream& kmerDBFile){
                kmerDBFile.seekg(0);                                                                    //      start at the beginning of the file
                
                //read version
-               string line = getline(kmerDBFile); gobble(kmerDBFile);
+               string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
                
                string seqName;
                int seqNumber;