sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sabundvector.cpp

diff --git a/sabundvector.cpp b/sabundvector.cpp
index b70c642643cfd746e63c236e328feb8e37d74a44..1bceec210779221ce0dfce33886b177e5250efd8 100644 (file)
--- a/sabundvector.cpp
+++ b/sabundvector.cpp
@@ -29,7 +29,7 @@ SAbundVector::SAbundVector(string id, vector<int> sav) : DataVector(id), data(sa
                }
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "SAbundVector");
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
 }
@@ -44,7 +44,7 @@ SAbundVector::SAbundVector(vector <int> dataVec, int mr, int nb, int ns) {
                numSeqs = ns;
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "SAbundVector");
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
 }
@@ -60,11 +60,13 @@ SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), n
        
                for(int i=1;i<=hold;i++){
                        f >> inputData;
+
                        set(i, inputData);
                }
+
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "SAbundVector");
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
 }
@@ -87,7 +89,7 @@ void SAbundVector::set(int sabund, int abundance){
                if(sabund > maxRank)    {       maxRank = sabund;               }
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "set");
+               m->errorOut(e, "SAbundVector", "set");
                exit(1);
        }
 }
@@ -112,7 +114,7 @@ void SAbundVector::push_back(int abundance){
                numSeqs += (maxRank * abundance);
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "push_back");
+               m->errorOut(e, "SAbundVector", "push_back");
                exit(1);
        }
 }
@@ -151,7 +153,13 @@ void SAbundVector::print(string prefix, ostream& output){
        }
        output << endl;
 }
-
+/***********************************************************************/
+void SAbundVector::clear(){
+       numBins = 0;
+       maxRank = 0;
+       numSeqs = 0;
+       data.clear();   
+}
 /***********************************************************************/
 void SAbundVector::print(ostream& output){
        try {
@@ -163,7 +171,7 @@ void SAbundVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "print");
+               m->errorOut(e, "SAbundVector", "print");
                exit(1);
        }
 }
@@ -192,18 +200,18 @@ RAbundVector SAbundVector::getRAbundVector(){
        try {
                RAbundVector rav;
        
-               for(int i=1;i<=data.size();i++){                
+               for(int i=1;i < data.size();i++){
                        for(int j=0;j<data[i];j++){
                                rav.push_back(i);
                        }
                }
                sort(rav.rbegin(), rav.rend());
-       
+
                rav.setLabel(label);
                return rav;
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "getRAbundVector");
+               m->errorOut(e, "SAbundVector", "getRAbundVector");
                exit(1);
        }
 }
@@ -238,7 +246,7 @@ OrderVector SAbundVector::getOrderVector(map<string,int>* hold = NULL){
                return ov;
        }
        catch(exception& e) {
-               errorOut(e, "SAbundVector", "getOrderVector");
+               m->errorOut(e, "SAbundVector", "getOrderVector");
                exit(1);
        }
 }