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

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index 65685d6a7e13c09f6563ebb3c2ea3f78dd3fd937..7c9fbe9c0eeda1472e09ce03c80cd5853103833e 100644 (file)
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -16,7 +16,7 @@
 
 InputData::InputData(string fName, string f) : format(f){
        m = MothurOut::getInstance();
-       openInputFile(fName, fileHandle);
+       m->openInputFile(fName, fileHandle);
        filename = fName;
        
 }
@@ -36,7 +36,7 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){
        try {
                m = MothurOut::getInstance();
                ifstream ofHandle;
-               openInputFile(orderFileName, ofHandle);
+               m->openInputFile(orderFileName, ofHandle);
                string name;
 
                int count = 0;
@@ -45,11 +45,11 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){
                        ofHandle >> name;
                        orderMap[name] = count;
                        count++;
-                       gobble(ofHandle);
+                       m->gobble(ofHandle);
                }
                ofHandle.close();
        
-               openInputFile(fName, fileHandle);
+               m->openInputFile(fName, fileHandle);
        }
        catch(exception& e) {
                m->errorOut(e, "InputData", "InputData");
@@ -65,7 +65,7 @@ ListVector* InputData::getListVector(){
                                list = new ListVector(fileHandle);
                        }else{ list = NULL;  }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return list;
                }
                else{
@@ -83,7 +83,7 @@ ListVector* InputData::getListVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -98,7 +98,7 @@ ListVector* InputData::getListVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete list;    }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }else{ list = NULL;  }
                        
@@ -127,7 +127,7 @@ ListVector* InputData::getListVector(string label, bool resetFP){
                        
                                while (fileHandle.eof() != true) {
                                        
-                                       list = new ListVector(fileHandle); gobble(fileHandle);
+                                       list = new ListVector(fileHandle); m->gobble(fileHandle);
                                        thisLabel = list->getLabel();
                                        
                                        //if you are at the last label
@@ -158,7 +158,7 @@ SharedListVector* InputData::getSharedListVector(){
                                SharedList = new SharedListVector(fileHandle);
                        }else{ SharedList = NULL;  }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return SharedList;
                }
                else{
@@ -176,7 +176,7 @@ SharedListVector* InputData::getSharedListVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -191,7 +191,7 @@ SharedListVector* InputData::getSharedListVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete SharedList;      }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }else{ SharedList = NULL;  }
@@ -220,7 +220,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){
                                SharedOrder = new SharedOrderVector(fileHandle);
                        }else{ SharedOrder = NULL;  }
                                
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return SharedOrder;
                        
                }else{
@@ -239,7 +239,7 @@ SharedOrderVector* InputData::getSharedOrderVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -254,7 +254,7 @@ SharedOrderVector* InputData::getSharedOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete SharedOrder;     }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }else{ SharedOrder = NULL;  }
@@ -295,7 +295,7 @@ OrderVector* InputData::getOrderVector(){
                                input = new SAbundVector(fileHandle);
                        }
                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        
                        output = new OrderVector();     
                        *output = (input->getOrderVector());
@@ -318,7 +318,7 @@ OrderVector* InputData::getOrderVector(string label){
        
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if((format == "list") || (format == "listorder")) {
@@ -332,7 +332,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }
                        else if (format == "shared")  {
@@ -346,7 +346,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -361,7 +361,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -376,7 +376,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -391,7 +391,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
 
@@ -431,7 +431,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
                                        return SharedList->getSharedRAbundVector();
                                }
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                                
                //this is created to signal to calling function that the input file is at eof
@@ -450,7 +450,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                ifstream in;
                string  thisLabel;
                
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if (format == "sharedfile")  {
@@ -468,7 +468,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                                                        delete SharedRAbund;
                                                }
                                        }else{  break;  }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
                        }else if (format == "shared") {
@@ -484,7 +484,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                                                        delete SharedList;
                                                }
                                        }else{  break;  }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
                        
@@ -525,7 +525,7 @@ SAbundVector* InputData::getSAbundVector(){
                                input = new SAbundVector(fileHandle);
                        }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
 
                        sabund = new SAbundVector();
                        *sabund = (input->getSAbundVector());
@@ -547,7 +547,7 @@ SAbundVector* InputData::getSAbundVector(string label){
        
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if (format == "list") {
@@ -561,7 +561,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }
                        else if (format == "shared")  {
@@ -575,7 +575,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -590,7 +590,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -605,7 +605,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -620,7 +620,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
 
@@ -664,7 +664,7 @@ RAbundVector* InputData::getRAbundVector(){
                                input = new SAbundVector(fileHandle);
                        }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
 
                        rabund = new RAbundVector();
                        *rabund = (input->getRAbundVector());
@@ -686,7 +686,7 @@ RAbundVector* InputData::getRAbundVector(string label){
        
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if (format == "list") {
@@ -700,7 +700,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }
                        else if (format == "shared")  {
@@ -714,7 +714,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -729,7 +729,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -744,7 +744,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -759,7 +759,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }