X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=inputdata.cpp;h=283fb7edc33856613612e10b0d293d0eea1f056d;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=7c9fbe9c0eeda1472e09ce03c80cd5853103833e;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/inputdata.cpp b/inputdata.cpp
index 7c9fbe9..283fb7e 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -16,6 +16,7 @@
 
 InputData::InputData(string fName, string f) : format(f){
 	m = MothurOut::getInstance();
+	globaldata = GlobalData::getInstance();
 	m->openInputFile(fName, fileHandle);
 	filename = fName;
 	
@@ -26,6 +27,8 @@ InputData::InputData(string fName, string f) : format(f){
 
 InputData::~InputData(){
 	fileHandle.close();
+	globaldata = GlobalData::getInstance();
+	globaldata->saveNextLabel = "";
 //	delete output;
 	
 }
@@ -35,6 +38,7 @@ 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;
@@ -451,7 +455,8 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 		string  thisLabel;
 		
 		m->openInputFile(filename, in);
-		
+		globaldata->saveNextLabel = "";
+	
 		if(in){
 			if (format == "sharedfile")  {
 				while (in.eof() != true) {
@@ -459,6 +464,7 @@ 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 {
@@ -503,7 +509,104 @@ 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);
+		globaldata->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(){