working on chimeras

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index d57f43586bceea765b01cfe4ca39b22d4e747c4e..1a7349492a99879dc3bb334893ff8ee7f36ae0bd 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -51,11 +51,11 @@ void DeCalculator::runMask(Sequence* seq) {
 }
 //***************************************************************************************************************
 //num is query's spot in querySeqs
-void DeCalculator::trimSeqs(Sequence* query, Sequence subject, map<int, int>& trim) {
+void DeCalculator::trimSeqs(Sequence* query, Sequence* subject, map<int, int>& trim) {
        try {
                
                string q = query->getAligned();
-               string s = subject.getAligned();
+               string s = subject->getAligned();
                
                int front = 0;
                for (int i = 0; i < q.length(); i++) {
@@ -131,7 +131,7 @@ vector<int>  DeCalculator::findWindows(Sequence* query, int front, int back, int
 }
 
 //***************************************************************************************************************
-vector<float> DeCalculator::calcObserved(Sequence* query, Sequence subject, vector<int> window, int size) {
+vector<float> DeCalculator::calcObserved(Sequence* query, Sequence* subject, vector<int> window, int size) {
        try {
                
                vector<float> temp;
@@ -139,7 +139,7 @@ vector<float> DeCalculator::calcObserved(Sequence* query, Sequence subject, vect
                for (int m = 0; m < window.size(); m++) {
                                                
                        string seqFrag = query->getAligned().substr(window[m], size);
-                       string seqFragsub = subject.getAligned().substr(window[m], size);
+                       string seqFragsub = subject->getAligned().substr(window[m], size);
        //cout << "start point = " << window[m] << " end point = " << window[m]+size << endl;                                           
                        int diff = 0;
                        for (int b = 0; b < seqFrag.length(); b++) {
@@ -162,7 +162,7 @@ vector<float> DeCalculator::calcObserved(Sequence* query, Sequence subject, vect
        }
 }
 //***************************************************************************************************************
-float DeCalculator::calcDist(Sequence* query, Sequence subject, int front, int back) {
+float DeCalculator::calcDist(Sequence* query, Sequence* subject, int front, int back) {
        try {
                
                //so you only look at the trimmed part of the sequence
@@ -170,7 +170,7 @@ float DeCalculator::calcDist(Sequence* query, Sequence subject, int front, int b
                        
                //from first startpoint with length back-front
                string seqFrag = query->getAligned().substr(front, cutoff);
-               string seqFragsub = subject.getAligned().substr(front, cutoff);
+               string seqFragsub = subject->getAligned().substr(front, cutoff);
                                                                                                                
                int diff = 0;
                for (int b = 0; b < seqFrag.length(); b++) {
@@ -234,7 +234,7 @@ vector<float> DeCalculator::calcFreq(vector<Sequence*> seqs, string filename) {
        try {
 
                vector<float> prob;
-               string freqfile = getRootName(filename) + "prob";
+               string freqfile = getRootName(filename) + "freq";
                ofstream outFreq;
                
                openOutputFile(freqfile, outFreq);
@@ -273,9 +273,12 @@ vector<float> DeCalculator::calcFreq(vector<Sequence*> seqs, string filename) {
                        if (Pi < 0) { Pi = 0.0; }
                        
                        //saves this for later
-                       outFreq << i+1 << '\t' << Pi << endl;
+                       outFreq << i+1 << '\t' << highFreq << endl;
                        
-                       prob.push_back(Pi); 
+                       if (h.count(i) > 0) {
+       cout << i+1 << '\t' << highFreq << endl;
+                               prob.push_back(Pi); 
+                       }
                }
                
                outFreq.close();
@@ -341,7 +344,7 @@ vector< vector<float> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vecto
                        //compare to every other sequence in template
                        for(int j = 0; j < i; j++){
                                
-                               Sequence subject = *(seqs[j]);
+                               Sequence* subject = seqs[j];
                                
                                map<int, int> trim;
                                map<int, int>::iterator it;