added diffs and percent parameters to cluster.fragments command

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 94b6c938009bb412ad62420bf6dfea2b6428e6e7..8d90a78a492e63ee97ede0b577e37fde39336fb4 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -290,10 +290,10 @@ vector<float> DeCalculator::calcFreq(vector<Sequence*> seqs, string filename) {
        try {
 
                vector<float> prob;
-               string freqfile = getRootName(filename) + "freq";
+               string freqfile = m->getRootName(filename) + "freq";
                ofstream outFreq;
                
-               openOutputFile(freqfile, outFreq);
+               m->openOutputFile(freqfile, outFreq);
                
                outFreq << "#" << m->getVersion() << endl;
                
@@ -688,6 +688,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                indexes.clear();
                
                vector<Sequence*> seqsMatches;  
+               
                vector<SeqDist> distsLeft;
                vector<SeqDist> distsRight;
                
@@ -759,14 +760,14 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        float distRight = distcalculator->getDist();
                        
                        SeqDist subjectLeft;
-                       subjectLeft.seq = db[j];
+                       subjectLeft.seq = NULL;
                        subjectLeft.dist = distLeft;
                        subjectLeft.index = j;
                        
                        distsLeft.push_back(subjectLeft);
                        
                        SeqDist subjectRight;
-                       subjectRight.seq = db[j];
+                       subjectRight.seq = NULL;
                        subjectRight.dist = distRight;
                        subjectRight.index = j;
                        
@@ -790,18 +791,18 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                int lasti = 0;
                for (int i = 0; i < distsLeft.size(); i++) {
                        //add left if you havent already
-                       it = seen.find(distsLeft[i].seq->getName());
+                       it = seen.find(db[distsLeft[i].index]->getName());
                        if (it == seen.end()) {  
                                dists.push_back(distsLeft[i]);
-                               seen[distsLeft[i].seq->getName()] = distsLeft[i].seq->getName();
+                               seen[db[distsLeft[i].index]->getName()] = db[distsLeft[i].index]->getName();
                                lastLeft =  distsLeft[i].dist;
                        }
 
                        //add right if you havent already
-                       it = seen.find(distsRight[i].seq->getName());
+                       it = seen.find(db[distsRight[i].index]->getName());
                        if (it == seen.end()) {  
                                dists.push_back(distsRight[i]);
-                               seen[distsRight[i].seq->getName()] = distsRight[i].seq->getName();
+                               seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
                                lastRight =  distsRight[i].dist;
                        }
                        
@@ -829,7 +830,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 //cout << numWanted << endl;
                for (int i = 0; i < numWanted; i++) {
 //cout << dists[i].seq->getName() << '\t' << dists[i].dist << endl;
-                       Sequence* temp = new Sequence(dists[i].seq->getName(), dists[i].seq->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
+                       Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
                        seqsMatches.push_back(temp);
                        indexes.push_back(dists[i].index);
                }
@@ -947,28 +948,35 @@ map<int, int> DeCalculator::trimSeqs(Sequence* query, vector<Sequence*> topMatch
                
                //save this spot if it is the farthest
                if (pos < rearPos) { rearPos = pos; }
-
-               //check to make sure that is not whole seq
-               if ((rearPos - frontPos - 1) <= 0) {  m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1);  }
-//cout << query->getName() << " front = " << frontPos << " rear = " << rearPos << endl;                
-               //trim query
-               string newAligned = query->getAligned();
-               newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
-               query->setAligned(newAligned);
-               
-               //trim topMatches
-               for (int i = 0; i < topMatches.size(); i++) {
-                       newAligned = topMatches[i]->getAligned();
-                       newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
-                       topMatches[i]->setAligned(newAligned);
-               }
                
                map<int, int> trimmedPos;
-               
-               for (int i = 0; i < newAligned.length(); i++) {
-                       trimmedPos[i] = i+frontPos;
+               //check to make sure that is not whole seq
+               if ((rearPos - frontPos - 1) <= 0) {  
+                       m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();  
+                       query->setAligned("");
+                       //trim topMatches
+                       for (int i = 0; i < topMatches.size(); i++) {
+                               topMatches[i]->setAligned("");
+                       }
+                       
+               }else {
+
+                       //trim query
+                       string newAligned = query->getAligned();
+                       newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
+                       query->setAligned(newAligned);
+                       
+                       //trim topMatches
+                       for (int i = 0; i < topMatches.size(); i++) {
+                               newAligned = topMatches[i]->getAligned();
+                               newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
+                               topMatches[i]->setAligned(newAligned);
+                       }
+                       
+                       for (int i = 0; i < newAligned.length(); i++) {
+                               trimmedPos[i] = i+frontPos;
+                       }
                }
-               
                return trimmedPos;
        }
        catch(exception& e) {