X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=inputdata.cpp;h=b237bb4fc55b0bacafa3815f9619f0345bd31492;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=4ed9c2711d2f11b0182ec165884d3747eeb0be80;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/inputdata.cpp b/inputdata.cpp
index 4ed9c27..b237bb4 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -10,7 +10,7 @@
 #include "inputdata.h"
 #include "ordervector.hpp"
 #include "listvector.hpp"
-#include "utilities.hpp"
+#include "rabundvector.hpp"
 
 /***********************************************************************/
 
@@ -24,7 +24,7 @@ InputData::InputData(string fName, string f) : format(f){
 
 
 InputData::~InputData(){
-	
+	fileHandle.close();
 //	delete output;
 	
 }
@@ -33,6 +33,7 @@ InputData::~InputData(){
 
 InputData::InputData(string fName, string orderFileName, string f) : format(f){
 	try {
+		
 		ifstream ofHandle;
 		openInputFile(orderFileName, ofHandle);
 		string name;
@@ -89,7 +90,7 @@ ListVector* InputData::getListVector(){
 SharedListVector* InputData::getSharedListVector(){
 	try {
 		if(fileHandle){
-			if (format == "shared"){
+			if (format == "shared")  {
 				SharedList = new SharedListVector(fileHandle);
 			}
 					
@@ -110,6 +111,33 @@ SharedListVector* InputData::getSharedListVector(){
 	}	
 }
 
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(){
+	try {
+		if(fileHandle){
+			if (format == "sharedfile")  {
+				SharedOrder = new SharedOrderVector(fileHandle);
+			}
+				
+			gobble(fileHandle);
+			return SharedOrder;
+			
+		}else{
+			return 0;
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+
 
 /***********************************************************************/
 
@@ -119,7 +147,7 @@ OrderVector* InputData::getOrderVector(){
 			if(format == "list") {
 				input = new ListVector(fileHandle);
 			}
-			else if(format == "shared") {
+			else if (format == "shared")  {
 				input = new SharedListVector(fileHandle);
 			}
 			else if(format == "rabund"){
@@ -138,7 +166,7 @@ OrderVector* InputData::getOrderVector(){
 			gobble(fileHandle);
 			output = new OrderVector();
 			*output = (input->getOrderVector());
-			//delete input;
+			
 			return output;
 		}
 		else{
@@ -154,6 +182,40 @@ OrderVector* InputData::getOrderVector(){
 		exit(1);
 	}	
 }
+/***********************************************************************/
+//this is used when you don't need the order vector
+vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
+	try {
+		if(fileHandle){
+			if (format == "sharedfile")  {
+				SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
+				if (SharedRAbund != NULL) {
+					return SharedRAbund->getSharedRAbundVectors();
+				}
+			}else if (format == "shared") {
+				SharedList = new SharedListVector(fileHandle);
+				if (SharedList != NULL) {
+					return SharedList->getSharedRAbundVector();
+				}
+			}
+			gobble(fileHandle);
+		}
+				
+		//this is created to signal to calling function that the input file is at eof
+		vector<SharedRAbundVector*> null;  null.push_back(NULL);
+		return null;
+		
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the InputData class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
 
 /***********************************************************************/
 
@@ -163,7 +225,7 @@ SAbundVector* InputData::getSAbundVector(){
 			if (format == "list") {
 				input = new ListVector(fileHandle);
 			}
-			else if(format == "shared") {
+			else if (format == "shared")  {
 				input = new SharedListVector(fileHandle);
 			}
 			else if(format == "rabund"){
@@ -198,3 +260,46 @@ SAbundVector* InputData::getSAbundVector(){
 }
 
 /***********************************************************************/
+RAbundVector* InputData::getRAbundVector(){
+	try {
+		if(fileHandle){
+			if (format == "list") {
+				input = new ListVector(fileHandle);
+			}
+			else if (format == "shared")  {
+				input = new SharedListVector(fileHandle);
+			}
+			else if(format == "rabund"){
+				input = new RAbundVector(fileHandle);
+			}
+			else if(format == "order"){			
+				input = new OrderVector(fileHandle);
+			}
+			else if(format == "sabund"){
+				input = new SAbundVector(fileHandle);
+			}
+					
+			gobble(fileHandle);
+
+			rabund = new RAbundVector();
+			*rabund = (input->getRAbundVector());
+
+			return rabund;
+		}
+		else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the InputData class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+/***********************************************************************/
+
+
+