changed random forest output filename

[mothur.git] / suffixdb.cpp

diff --git a/suffixdb.cpp b/suffixdb.cpp
index 5bcd8e96c0be725ee978ba74a4d32bb36b3aa4e0..4fc342dd8bd26f7809ef93ce57da1b5563ee4ad1 100644 (file)
--- a/suffixdb.cpp
+++ b/suffixdb.cpp
@@ -22,41 +22,64 @@
 
 /**************************************************************************************************/
 
-SuffixDB::SuffixDB(string fastaFileName) : Database(fastaFileName) {
-
+SuffixDB::SuffixDB(int numSeqs) : Database() {
        suffixForest.resize(numSeqs);
-       mothurOut("Generating the suffix tree database...\t");  cout.flush();
-       for(int i=0;i<numSeqs;i++){                                                             //      The parent class' constructor generates the vector of
-               suffixForest[i].loadSequence(templateSequences[i]);     //      template Sequence objects.  Here each of these objects
-       }                                                                                                               //      is used to generate a suffix tree, aka the suffix forest
-       mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
-
+       count = 0;
 }
-
 /**************************************************************************************************/
 
-Sequence SuffixDB::findClosestSequence(Sequence* candidateSeq){
+SuffixDB::SuffixDB() : Database() {
+       count = 0;
+}
 
-       int minValue = 2000;
-       int closestSequenceNo = 0;
-       string processedSeq = candidateSeq->convert2ints();             //      the candidate sequence needs to be a string of ints
-       for(int i=0;i<suffixForest.size();i++){                                 //      scan through the forest and see what the minimum
-               int count = suffixForest[i].countSuffixes(processedSeq, minValue);      //      return score is and keep track of the
-               if(count == minValue){                                                          //      template sequence index that corresponds to that score
-                       closestSequenceNo = i;
+/**************************************************************************************************/
+//assumes sequences have been added using addSequence
+vector<int> SuffixDB::findClosestSequences(Sequence* candidateSeq, int num){
+       try {
+               vector<int> topMatches;
+               string processedSeq = candidateSeq->convert2ints();             //      the candidate sequence needs to be a string of ints
+               
+               vector<seqMatch> seqMatches;
+               for(int i=0;i<suffixForest.size();i++){                                 //      scan through the forest and see what the minimum
+                       int count = suffixForest[i].countSuffixes(processedSeq);        //      return score is and keep track of the
+                       seqMatch temp(i, count);
+                       seqMatches.push_back(temp);
+               }
+               
+               //sorts putting smallest matches first
+               sort(seqMatches.begin(), seqMatches.end(), compareSeqMatchesReverse);
+               
+               searchScore = seqMatches[0].match;
+               searchScore = 100 * (1. - searchScore / (float)processedSeq.length());
+               
+               //save top matches
+               for (int i = 0; i < num; i++) {
+                       topMatches.push_back(seqMatches[i].seq);
                }
+
+               //      return the Sequence object that has the minimum score
+               return topMatches;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SuffixDB", "findClosestSequences");
+               exit(1);
+       }       
+}
+/**************************************************************************************************/
+//adding the sequences generates the db
+void SuffixDB::addSequence(Sequence seq) {
+       try {
+               suffixForest[count].loadSequence(seq);          
+               count++;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SuffixDB", "addSequence");
+               exit(1);
        }
-       searchScore = 100 * (1. - minValue / (float)processedSeq.length());
-       return templateSequences[closestSequenceNo];                    //      return the Sequence object that has the minimum score
-       
 }
-
 /**************************************************************************************************/
 
 SuffixDB::~SuffixDB(){                                                                                                         
-       
        for (int i = (suffixForest.size()-1); i >= 0; i--) {  suffixForest.pop_back();  }
-       // templateSequences.clear();
-
 }
 /**************************************************************************************************/