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

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index cc3cd8df4205e2f37182a8a80037bc02bb37ca45..49780314bca4d40be6a96a9593831b39317faaca 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -52,9 +52,9 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
 /***********************************************************************/
 void SharedListVector::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--;                              }
@@ -79,7 +79,7 @@ string SharedListVector::get(int index){
 void SharedListVector::push_back(string seqNames){
        try {
                data.push_back(seqNames);
-               int nNames = getNumNames(seqNames);
+               int nNames = m->getNumNames(seqNames);
        
                numBins++;
        
@@ -141,7 +141,7 @@ RAbundVector SharedListVector::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);
                }
        
@@ -171,7 +171,7 @@ SAbundVector SharedListVector::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);
@@ -194,7 +194,7 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                order->setLabel(label);
        
                for(int i=0;i<numBins;i++){
-                       int binSize = getNumNames(get(i));      //find number of individual in given bin        
+                       int binSize = m->getNumNames(get(i));   //find number of individual in given bin        
                        names = get(i);
                        while (names.find_first_of(',') != -1) { 
                                name = names.substr(0,names.find_first_of(','));
@@ -275,7 +275,7 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                        finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-                       if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
+                       if (m->inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
                                lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
                        }
                }
@@ -331,7 +331,7 @@ OrderVector SharedListVector::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);
                                }