changing command name classify.shared to classifyrf.shared

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index 65685d6a7e13c09f6563ebb3c2ea3f78dd3fd937..8b1829a3db697df21b3d0f64bf6be6cfea15c536 100644 (file)
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -16,18 +16,15 @@
 
 InputData::InputData(string fName, string f) : format(f){
        m = MothurOut::getInstance();
-       openInputFile(fName, fileHandle);
+       m->openInputFile(fName, fileHandle);
        filename = fName;
-       
+       m->saveNextLabel = "";
 }
-
 /***********************************************************************/
 
-
 InputData::~InputData(){
        fileHandle.close();
-//     delete output;
-       
+       m->saveNextLabel = "";
 }
 
 /***********************************************************************/
@@ -36,7 +33,7 @@ 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 +42,13 @@ 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);
+               m->saveNextLabel = "";
+               
        }
        catch(exception& e) {
                m->errorOut(e, "InputData", "InputData");
@@ -65,7 +64,7 @@ ListVector* InputData::getListVector(){
                                list = new ListVector(fileHandle);
                        }else{ list = NULL;  }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return list;
                }
                else{
@@ -83,7 +82,7 @@ ListVector* InputData::getListVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -98,7 +97,7 @@ 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 +126,7 @@ 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 +157,7 @@ SharedListVector* InputData::getSharedListVector(){
                                SharedList = new SharedListVector(fileHandle);
                        }else{ SharedList = NULL;  }
                                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return SharedList;
                }
                else{
@@ -176,7 +175,7 @@ SharedListVector* InputData::getSharedListVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -191,7 +190,7 @@ 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 +219,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){
                                SharedOrder = new SharedOrderVector(fileHandle);
                        }else{ SharedOrder = NULL;  }
                                
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        return SharedOrder;
                        
                }else{
@@ -239,7 +238,7 @@ SharedOrderVector* InputData::getSharedOrderVector(string label){
        try {
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
 
@@ -254,7 +253,7 @@ 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;  }
@@ -294,8 +293,8 @@ OrderVector* InputData::getOrderVector(){
                        else if(format == "sabund"){
                                input = new SAbundVector(fileHandle);
                        }
-                       
-                       gobble(fileHandle);
+                                               
+                       m->gobble(fileHandle);
                        
                        output = new OrderVector();     
                        *output = (input->getOrderVector());
@@ -318,7 +317,7 @@ 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 +331,7 @@ 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 +345,7 @@ 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 +360,7 @@ 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 +375,7 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -391,12 +390,12 @@ OrderVector* InputData::getOrderVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
 
                        }
-                       
+                                               
                        in.close();             
 
                        output = new OrderVector();
@@ -427,11 +426,12 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
                                }
                        }else if (format == "shared") {
                                SharedList = new SharedListVector(fileHandle);
+                               
                                if (SharedList != NULL) {
                                        return SharedList->getSharedRAbundVector();
                                }
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                                
                //this is created to signal to calling function that the input file is at eof
@@ -450,8 +450,9 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                ifstream in;
                string  thisLabel;
                
-               openInputFile(filename, in);
-               
+               m->openInputFile(filename, in);
+               m->saveNextLabel = "";
+       
                if(in){
                        if (format == "sharedfile")  {
                                while (in.eof() != true) {
@@ -459,6 +460,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                                        SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
                                        if (SharedRAbund != NULL) {
                                                thisLabel = SharedRAbund->getLabel();
+                                       
                                                //if you are at the last label
                                                if (thisLabel == label) {  in.close(); return SharedRAbund->getSharedRAbundVectors();  }
                                                else {
@@ -468,13 +470,14 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                                                        delete SharedRAbund;
                                                }
                                        }else{  break;  }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
                        }else if (format == "shared") {
                                while (in.eof() != true) {
                                        
                                        SharedList = new SharedListVector(in);
+                                       
                                        if (SharedList != NULL) {
                                                thisLabel = SharedList->getLabel();
                                                //if you are at the last label
@@ -484,7 +487,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
                                                        delete SharedList;
                                                }
                                        }else{  break;  }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
                        
@@ -503,7 +506,104 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
        }
 }
 
-
+/***********************************************************************/
+//this is used when you don't need the order vector
+vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(){
+       try {
+               if(fileHandle){
+                       if (format == "relabund")  {
+                               SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(fileHandle);
+                               if (SharedRelAbund != NULL) {
+                                       return SharedRelAbund->getSharedRAbundFloatVectors();
+                               }
+                       }else if (format == "sharedfile")  {
+                               SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
+                               if (SharedRAbund != NULL) {
+                                       vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors(); 
+                                       vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup); 
+                                       for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+                                       return lookupFloat;  
+                               }
+                                               
+                       }
+                       m->gobble(fileHandle);
+               }
+                               
+               //this is created to signal to calling function that the input file is at eof
+               vector<SharedRAbundFloatVector*> null;  null.push_back(NULL);
+               return null;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "InputData", "getSharedRAbundFloatVectors");
+               exit(1);
+       }
+}
+/***********************************************************************/
+vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(string label){
+       try {
+               ifstream in;
+               string  thisLabel;
+               
+               m->openInputFile(filename, in);
+               m->saveNextLabel = "";
+               
+               if(in){
+                       if (format == "relabund")  {
+                               while (in.eof() != true) {
+                                       
+                                       SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(in);
+                                       if (SharedRelAbund != NULL) {
+                                               thisLabel = SharedRelAbund->getLabel();
+                                               //if you are at the last label
+                                               if (thisLabel == label) {  in.close(); return SharedRelAbund->getSharedRAbundFloatVectors();  }
+                                               else {
+                                                       //so you don't loose this memory
+                                                       vector<SharedRAbundFloatVector*> lookup = SharedRelAbund->getSharedRAbundFloatVectors(); 
+                                                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                                                       delete SharedRelAbund;
+                                               }
+                                       }else{  break;  }
+                                       m->gobble(in);
+                               }
+                       }else if (format == "sharedfile")  {
+                               while (in.eof() != true) {
+                                       
+                                       SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
+                                       if (SharedRAbund != NULL) {
+                                               thisLabel = SharedRAbund->getLabel();
+                                               
+                                               //if you are at the last label
+                                               if (thisLabel == label) {  
+                                                       in.close(); 
+                                                       vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors(); 
+                                                       vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup); 
+                                                       for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+                                                       return lookupFloat;  
+                                               }else {
+                                                       //so you don't loose this memory
+                                                       vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors(); 
+                                                       for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+                                                       delete SharedRAbund;
+                                               }
+                                       }else{  break;  }
+                                       m->gobble(in);
+                               }
+                       }       
+               }
+               
+                               
+               //this is created to signal to calling function that the input file is at eof
+               vector<SharedRAbundFloatVector*> null;  null.push_back(NULL);
+               in.close();
+               return null;
+       
+       }
+       catch(exception& e) {
+               m->errorOut(e, "InputData", "getSharedRAbundFloatVectors");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 SAbundVector* InputData::getSAbundVector(){
@@ -523,9 +623,8 @@ SAbundVector* InputData::getSAbundVector(){
                        }
                        else if(format == "sabund"){
                                input = new SAbundVector(fileHandle);
-                       }
-                                       
-                       gobble(fileHandle);
+                       }                                       
+                       m->gobble(fileHandle);
 
                        sabund = new SAbundVector();
                        *sabund = (input->getSAbundVector());
@@ -547,7 +646,7 @@ SAbundVector* InputData::getSAbundVector(string label){
        
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if (format == "list") {
@@ -561,7 +660,7 @@ 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 +674,7 @@ 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 +689,7 @@ 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 +704,7 @@ 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 +719,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
 
@@ -663,8 +762,8 @@ RAbundVector* InputData::getRAbundVector(){
                        else if(format == "sabund"){
                                input = new SAbundVector(fileHandle);
                        }
-                                       
-                       gobble(fileHandle);
+                       
+                       m->gobble(fileHandle);
 
                        rabund = new RAbundVector();
                        *rabund = (input->getRAbundVector());
@@ -686,7 +785,7 @@ RAbundVector* InputData::getRAbundVector(string label){
        
                ifstream in;
                string  thisLabel;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                if(in){
                        if (format == "list") {
@@ -700,7 +799,7 @@ 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 +813,7 @@ 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 +828,7 @@ 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 +843,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
 
                        }
@@ -759,11 +858,12 @@ RAbundVector* InputData::getRAbundVector(string label){
                                        if (thisLabel == label) {  break;  }
                                        //so you don't loose this memory
                                        else {  delete input;   }
-                                       gobble(in);
+                                       m->gobble(in);
                                        
                                }
 
-                       }
+                       }                       
+                       
                        
                        in.close();