X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=inputdata.cpp;h=8b1829a3db697df21b3d0f64bf6be6cfea15c536;hp=7c9fbe9c0eeda1472e09ce03c80cd5853103833e;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6

diff --git a/inputdata.cpp b/inputdata.cpp
index 7c9fbe9..8b1829a 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -18,16 +18,13 @@ InputData::InputData(string fName, string f) : format(f){
 	m = MothurOut::getInstance();
 	m->openInputFile(fName, fileHandle);
 	filename = fName;
-	
+	m->saveNextLabel = "";
 }
-
 /***********************************************************************/
 
-
 InputData::~InputData(){
 	fileHandle.close();
-//	delete output;
-	
+	m->saveNextLabel = "";
 }
 
 /***********************************************************************/
@@ -50,6 +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");
@@ -294,7 +293,7 @@ OrderVector* InputData::getOrderVector(){
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
 			}
-			
+						
 			m->gobble(fileHandle);
 			
 			output = new OrderVector();	
@@ -396,7 +395,7 @@ OrderVector* InputData::getOrderVector(string label){
 				}
 
 			}
-			
+						
 			in.close();		
 
 			output = new OrderVector();
@@ -427,6 +426,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
 				}
 			}else if (format == "shared") {
 				SharedList = new SharedListVector(fileHandle);
+				
 				if (SharedList != NULL) {
 					return SharedList->getSharedRAbundVector();
 				}
@@ -451,7 +451,8 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 		string  thisLabel;
 		
 		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 {
@@ -475,6 +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
@@ -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(){
@@ -523,8 +623,7 @@ SAbundVector* InputData::getSAbundVector(){
 			}
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
-			}
-					
+			}					
 			m->gobble(fileHandle);
 
 			sabund = new SAbundVector();
@@ -663,7 +762,7 @@ RAbundVector* InputData::getRAbundVector(){
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
 			}
-					
+			
 			m->gobble(fileHandle);
 
 			rabund = new RAbundVector();
@@ -763,7 +862,8 @@ RAbundVector* InputData::getRAbundVector(string label){
 					
 				}
 
-			}
+			}			
+			
 			
 			in.close();