moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / listvector.cpp

diff --git a/listvector.cpp b/listvector.cpp
index 94ca02662bc1e59f61312e7c33d2244faa30e3ae..4bb45b7f83d9c811a018f5c475fc557a9f65287f 100644 (file)
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -28,7 +28,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
        try {
                for(int i=0;i<data.size();i++){
                        if(data[i] != ""){
-                               int binSize = getNumNames(data[i]);
+                               int binSize = m->getNumNames(data[i]);
                                numBins = i+1;
                                if(binSize > maxRank)   {       maxRank = binSize;      }
                                numSeqs += binSize;
@@ -56,7 +56,7 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
                        set(i, inputData);
                }
                
-               gobble(f);
+               m->gobble(f);
        }
        catch(exception& e) {
                m->errorOut(e, "ListVector", "ListVector");
@@ -68,9 +68,9 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 
 void ListVector::set(int binNumber, string seqNames){
        try {
-               int nNames_old = getNumNames(data[binNumber]);
+               int nNames_old = m->getNumNames(data[binNumber]);
                data[binNumber] = seqNames;
-               int nNames_new = getNumNames(seqNames);
+               int nNames_new = m->getNumNames(seqNames);
        
                if(nNames_old == 0)                     {       numBins++;                              }
                if(nNames_new == 0)                     {       numBins--;                              }
@@ -95,7 +95,7 @@ string ListVector::get(int index){
 void ListVector::push_back(string seqNames){
        try {
                data.push_back(seqNames);
-               int nNames = getNumNames(seqNames);
+               int nNames = m->getNumNames(seqNames);
        
                numBins++;
        
@@ -157,7 +157,7 @@ RAbundVector ListVector::getRAbundVector(){
                RAbundVector rav;
        
                for(int i=0;i<data.size();i++){
-                       int binSize = getNumNames(data[i]);
+                       int binSize = m->getNumNames(data[i]);
                        rav.push_back(binSize);
                }
        
@@ -187,7 +187,7 @@ SAbundVector ListVector::getSAbundVector(){
                SAbundVector sav(maxRank+1);
        
                for(int i=0;i<data.size();i++){
-                       int binSize = getNumNames(data[i]);     
+                       int binSize = m->getNumNames(data[i]);  
                        sav.set(binSize, sav.get(binSize) + 1); 
                }
                sav.set(0, 0);
@@ -210,7 +210,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
                        OrderVector ov;
                
                        for(int i=0;i<data.size();i++){
-                               int binSize = getNumNames(data[i]);             
+                               int binSize = m->getNumNames(data[i]);          
                                for(int j=0;j<binSize;j++){
                                        ov.push_back(i);
                                }