X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=inputdata.cpp;h=cbf44ed11a96a03c251fcc3025b185c2020c2830;hb=c53c53b0280452e1c3a087fbf807b2e508cd66c4;hp=e5513ab99610f79762f0809c886cf326ad2cda5e;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/inputdata.cpp b/inputdata.cpp
index e5513ab..cbf44ed 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -3,20 +3,21 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 11/18/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "inputdata.h"
 #include "ordervector.hpp"
 #include "listvector.hpp"
-#include "utilities.hpp"
+#include "rabundvector.hpp"
 
 /***********************************************************************/
 
 InputData::InputData(string fName, string f) : format(f){
 	
 	openInputFile(fName, fileHandle);
+	filename = fName;
 	
 }
 
@@ -24,7 +25,7 @@ InputData::InputData(string fName, string f) : format(f){
 
 
 InputData::~InputData(){
-	
+	fileHandle.close();
 //	delete output;
 	
 }
@@ -33,6 +34,7 @@ InputData::~InputData(){
 
 InputData::InputData(string fName, string orderFileName, string f) : format(f){
 	try {
+		
 		ifstream ofHandle;
 		openInputFile(orderFileName, ofHandle);
 		string name;
@@ -50,13 +52,9 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){
 		openInputFile(fName, fileHandle);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InputData", "InputData");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InputData class function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 /***********************************************************************/
 
@@ -71,25 +69,60 @@ ListVector* InputData::getListVector(){
 			return list;
 		}
 		else{
-			return 0;
+			return NULL;
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InputData", "getListVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+
+ListVector* InputData::getListVector(string label){
+	try {
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+
+			if (format == "list") {
+			
+				while (in.eof() != true) {
+					
+					list = new ListVector(in);
+					thisLabel = list->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete list;	}
+					gobble(in);
+				}
+			}
+			
+			in.close();
+			return list;
+		}
+		else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getListVector");
 		exit(1);
-	}	
+	}
 }
 
+
 /***********************************************************************/
 
 SharedListVector* InputData::getSharedListVector(){
 	try {
 		if(fileHandle){
-			if (format == "shared"){
+			if (format == "shared")  {
 				SharedList = new SharedListVector(fileHandle);
 			}
 					
@@ -97,29 +130,127 @@ SharedListVector* InputData::getSharedListVector(){
 			return SharedList;
 		}
 		else{
-			return 0;
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSharedListVector");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+SharedListVector* InputData::getSharedListVector(string label){
+	try {
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+
+			if (format == "shared")  {
+			
+				while (in.eof() != true) {
+					
+					SharedList = new SharedListVector(in);
+					thisLabel = SharedList->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete SharedList;	}
+					gobble(in);
+				}
+
+			}
+				
+			in.close();
+			return SharedList;
+			
+		}else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSharedListVector");
+		exit(1);
+	}
+}
+
+
+
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(){
+	try {
+		if(fileHandle){
+			if (format == "sharedfile")  {
+				SharedOrder = new SharedOrderVector(fileHandle);
+			}
+				
+			gobble(fileHandle);
+			return SharedOrder;
+			
+		}else{
+			return NULL;
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InputData", "getSharedOrderVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(string label){
+	try {
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+
+			if (format == "sharedfile")  {
+			
+				while (in.eof() != true) {
+					
+					SharedOrder = new SharedOrderVector(in);
+					thisLabel = SharedOrder->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete SharedOrder;	}
+					gobble(in);
+				}
+
+			}
+				
+			in.close();
+			return SharedOrder;
+			
+		}else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSharedOrderVector");
 		exit(1);
-	}	
+	}
 }
 
 
+
 /***********************************************************************/
 
 OrderVector* InputData::getOrderVector(){
 	try {
 		if(fileHandle){
-			if(format == "list") {
+			if((format == "list") || (format == "listorder")) {
 				input = new ListVector(fileHandle);
 			}
-			else if(format == "shared") {
+			else if (format == "shared")  {
 				input = new SharedListVector(fileHandle);
 			}
 			else if(format == "rabund"){
@@ -131,30 +262,215 @@ OrderVector* InputData::getOrderVector(){
 			else if(format == "sabund"){
 				input = new SAbundVector(fileHandle);
 			}
-			else if(format == "listorder"){					
-				input = new ListVector(fileHandle); 
-			}
-		
+					
 			gobble(fileHandle);
 			output = new OrderVector();
 			*output = (input->getOrderVector());
-			//delete input;
+			
+			return output;
+		}
+		else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getOrderVector");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+OrderVector* InputData::getOrderVector(string label){
+	try {
+	
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+			if((format == "list") || (format == "listorder")) {
+			
+				while (in.eof() != true) {
+					
+					input = new ListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+			}
+			else if (format == "shared")  {
+				
+				while (in.eof() != true) {
+					
+					input = new SharedListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "rabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new RAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "order"){			
+				
+				while (in.eof() != true) {
+					
+					input = new OrderVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "sabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new SAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+					
+				}
+
+			}
+			
+			in.close();		
+
+			output = new OrderVector();
+			*output = (input->getOrderVector());
+			
 			return output;
+
 		}
 		else{
-			return 0;
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "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 getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InputData", "getSharedRAbundVectors");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
+	try {
+		ifstream in;
+		string  thisLabel;
+		
+		openInputFile(filename, in);
+		
+		if(in){
+			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(); return SharedRAbund->getSharedRAbundVectors();  }
+						else {
+							//so you don't loose this memory
+							vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors(); 
+							for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+							delete SharedRAbund;
+						}
+					}else{  break;  }
+					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
+						if (thisLabel == label) {  in.close(); return SharedList->getSharedRAbundVector();  }
+						else {
+							//so you don't loose this memory
+							delete SharedList;
+						}
+					}else{  break;  }
+					gobble(in);
+					
+				}
+			
+			}
+		}
+				
+		//this is created to signal to calling function that the input file is at eof
+		vector<SharedRAbundVector*> null;  null.push_back(NULL);
+		in.close();
+		return null;
+	
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSharedRAbundVectors");
 		exit(1);
-	}	
+	}
 }
 
+
 /***********************************************************************/
 
 SAbundVector* InputData::getSAbundVector(){
@@ -163,7 +479,7 @@ 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"){
@@ -184,17 +500,256 @@ SAbundVector* InputData::getSAbundVector(){
 			return sabund;
 		}
 		else{
-			return 0;
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSAbundVector");
+		exit(1);
+	}
+}
+/***********************************************************************/
+SAbundVector* InputData::getSAbundVector(string label){
+	try {
+	
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+			if (format == "list") {
+			
+				while (in.eof() != true) {
+					
+					input = new ListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+			}
+			else if (format == "shared")  {
+				
+				while (in.eof() != true) {
+					
+					input = new SharedListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "rabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new RAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "order"){			
+				
+				while (in.eof() != true) {
+					
+					input = new OrderVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "sabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new SAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+					
+				}
+
+			}
+			
+			in.close();		
+
+			sabund = new SAbundVector();
+			*sabund = (input->getSAbundVector());
+
+			return sabund;
+
+		}
+		else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getSAbundVector");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+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 getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InputData", "getRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+RAbundVector* InputData::getRAbundVector(string label){
+	try {
+	
+		ifstream in;
+		string  thisLabel;
+		openInputFile(filename, in);
+		
+		if(in){
+			if (format == "list") {
+			
+				while (in.eof() != true) {
+					
+					input = new ListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+			}
+			else if (format == "shared")  {
+				
+				while (in.eof() != true) {
+					
+					input = new SharedListVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "rabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new RAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "order"){			
+				
+				while (in.eof() != true) {
+					
+					input = new OrderVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+				}
+
+			}
+			else if(format == "sabund"){
+				
+				while (in.eof() != true) {
+					
+					input = new SAbundVector(in);
+					thisLabel = input->getLabel();
+					
+					//if you are at the last label
+					if (thisLabel == label) {  break;  }
+					//so you don't loose this memory
+					else {	delete input;	}
+					gobble(in);
+					
+				}
+
+			}
+			
+			in.close();		
+
+			rabund = new RAbundVector();
+			*rabund = (input->getRAbundVector());
+
+			return rabund;
+		}
+		else{
+			return NULL;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "InputData", "getRAbundVector");
 		exit(1);
-	}	
+	}
 }
 
 /***********************************************************************/
+
+
+