X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=inputdata.cpp;h=8b1829a3db697df21b3d0f64bf6be6cfea15c536;hp=5d1542739b0b0b6d6e730a5e84654468e3ca819f;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hpb=e99751591aa21705e58edda87383457b9738dd9e

diff --git a/inputdata.cpp b/inputdata.cpp
index 5d15427..8b1829a 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -16,21 +16,15 @@
 
 InputData::InputData(string fName, string f) : format(f){
 	m = MothurOut::getInstance();
-	globaldata = GlobalData::getInstance();
 	m->openInputFile(fName, fileHandle);
 	filename = fName;
-	
+	m->saveNextLabel = "";
 }
-
 /***********************************************************************/
 
-
 InputData::~InputData(){
 	fileHandle.close();
-	globaldata = GlobalData::getInstance();
-	globaldata->saveNextLabel = "";
-//	delete output;
-	
+	m->saveNextLabel = "";
 }
 
 /***********************************************************************/
@@ -38,7 +32,6 @@ InputData::~InputData(){
 InputData::InputData(string fName, string orderFileName, string f) : format(f){
 	try {
 		m = MothurOut::getInstance();
-		globaldata = GlobalData::getInstance();
 		ifstream ofHandle;
 		m->openInputFile(orderFileName, ofHandle);
 		string name;
@@ -54,6 +47,8 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){
 		ofHandle.close();
 	
 		m->openInputFile(fName, fileHandle);
+		m->saveNextLabel = "";
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "InputData", "InputData");
@@ -298,7 +293,7 @@ OrderVector* InputData::getOrderVector(){
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
 			}
-			
+						
 			m->gobble(fileHandle);
 			
 			output = new OrderVector();	
@@ -400,7 +395,7 @@ OrderVector* InputData::getOrderVector(string label){
 				}
 
 			}
-			
+						
 			in.close();		
 
 			output = new OrderVector();
@@ -431,6 +426,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
 				}
 			}else if (format == "shared") {
 				SharedList = new SharedListVector(fileHandle);
+				
 				if (SharedList != NULL) {
 					return SharedList->getSharedRAbundVector();
 				}
@@ -455,7 +451,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 		string  thisLabel;
 		
 		m->openInputFile(filename, in);
-		globaldata->saveNextLabel = "";
+		m->saveNextLabel = "";
 	
 		if(in){
 			if (format == "sharedfile")  {
@@ -481,6 +477,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 				while (in.eof() != true) {
 					
 					SharedList = new SharedListVector(in);
+					
 					if (SharedList != NULL) {
 						thisLabel = SharedList->getLabel();
 						//if you are at the last label
@@ -519,6 +516,15 @@ vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(){
 				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);
 		}
@@ -540,7 +546,7 @@ vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(string l
 		string  thisLabel;
 		
 		m->openInputFile(filename, in);
-		globaldata->saveNextLabel = "";
+		m->saveNextLabel = "";
 		
 		if(in){
 			if (format == "relabund")  {
@@ -560,8 +566,32 @@ vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(string l
 					}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);
@@ -593,8 +623,7 @@ SAbundVector* InputData::getSAbundVector(){
 			}
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
-			}
-					
+			}					
 			m->gobble(fileHandle);
 
 			sabund = new SAbundVector();
@@ -733,7 +762,7 @@ RAbundVector* InputData::getRAbundVector(){
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
 			}
-					
+			
 			m->gobble(fileHandle);
 
 			rabund = new RAbundVector();
@@ -833,7 +862,8 @@ RAbundVector* InputData::getRAbundVector(string label){
 					
 				}
 
-			}
+			}			
+			
 			
 			in.close();