#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);
-
+ m = MothurOut::getInstance();
+ m->openInputFile(fName, fileHandle);
+ filename = fName;
+ m->saveNextLabel = "";
}
-
/***********************************************************************/
-
InputData::~InputData(){
-
-// delete output;
-
+ fileHandle.close();
+ m->saveNextLabel = "";
}
/***********************************************************************/
InputData::InputData(string fName, string orderFileName, string f) : format(f){
try {
-
+ m = MothurOut::getInstance();
ifstream ofHandle;
- openInputFile(orderFileName, ofHandle);
+ m->openInputFile(orderFileName, ofHandle);
string name;
int count = 0;
ofHandle >> name;
orderMap[name] = count;
count++;
- gobble(ofHandle);
+ m->gobble(ofHandle);
}
ofHandle.close();
- openInputFile(fName, fileHandle);
+ m->openInputFile(fName, fileHandle);
+ m->saveNextLabel = "";
+
}
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";
+ m->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);
- }
}
/***********************************************************************/
ListVector* InputData::getListVector(){
try {
- if(fileHandle){
+ if(!fileHandle.eof()){
if(format == "list") {
list = new ListVector(fileHandle);
- }
+ }else{ list = NULL; }
- gobble(fileHandle);
+ m->gobble(fileHandle);
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";
+ m->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;
+ m->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; }
+ m->gobble(in);
+ }
+ }else{ list = NULL; }
+
+ in.close();
+ return list;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getListVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+ListVector* InputData::getListVector(string label, bool resetFP){
+ try {
+ string thisLabel;
+ fileHandle.clear();
+ fileHandle.seekg(0);
+
+ if(fileHandle){
+
+ if (format == "list") {
+
+ while (fileHandle.eof() != true) {
+
+ list = new ListVector(fileHandle); m->gobble(fileHandle);
+ thisLabel = list->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete list; }
+ }
+ }else{ list = NULL; }
+
+ return list;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getListVector");
exit(1);
- }
+ }
}
/***********************************************************************/
if(fileHandle){
if (format == "shared") {
SharedList = new SharedListVector(fileHandle);
- }
+ }else{ SharedList = NULL; }
- gobble(fileHandle);
+ m->gobble(fileHandle);
return SharedList;
}
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";
+ m->errorOut(e, "InputData", "getSharedListVector");
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";
+}
+/***********************************************************************/
+
+SharedListVector* InputData::getSharedListVector(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+ m->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; }
+ m->gobble(in);
+ }
+
+ }else{ SharedList = NULL; }
+
+ in.close();
+ return SharedList;
+
+ }else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getSharedListVector");
exit(1);
- }
+ }
}
+
+
/***********************************************************************/
SharedOrderVector* InputData::getSharedOrderVector(){
if(fileHandle){
if (format == "sharedfile") {
SharedOrder = new SharedOrderVector(fileHandle);
- }
+ }else{ SharedOrder = NULL; }
- gobble(fileHandle);
+ m->gobble(fileHandle);
return SharedOrder;
}else{
- return 0;
+ return NULL;
}
}
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";
+ m->errorOut(e, "InputData", "getSharedOrderVector");
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";
+}
+
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+ m->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; }
+ m->gobble(in);
+ }
+
+ }else{ SharedOrder = NULL; }
+
+ in.close();
+ return SharedOrder;
+
+ }else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->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 == "sabund"){
input = new SAbundVector(fileHandle);
}
- else if(format == "listorder"){
- input = new ListVector(fileHandle);
- }
+
+ m->gobble(fileHandle);
+
+ output = new OrderVector();
+ *output = (input->getOrderVector());
- gobble(fileHandle);
+ return output;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getOrderVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+OrderVector* InputData::getOrderVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->gobble(in);
+
+ }
+
+ }
+
+ in.close();
+
output = new OrderVector();
*output = (input->getOrderVector());
return output;
+
}
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";
+ m->errorOut(e, "InputData", "getOrderVector");
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";
+}
+
+/***********************************************************************/
+//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();
+ }
+ }
+ m->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) {
+ m->errorOut(e, "InputData", "getSharedRAbundVectors");
exit(1);
- }
+ }
+}
+/***********************************************************************/
+vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+
+ m->openInputFile(filename, in);
+ m->saveNextLabel = "";
+
+ 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; }
+ m->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; }
+ m->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) {
+ m->errorOut(e, "InputData", "getSharedRAbundVectors");
+ exit(1);
+ }
}
+/***********************************************************************/
+//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(){
}
else if(format == "sabund"){
input = new SAbundVector(fileHandle);
+ }
+ m->gobble(fileHandle);
+
+ sabund = new SAbundVector();
+ *sabund = (input->getSAbundVector());
+
+ return sabund;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getSAbundVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+SAbundVector* InputData::getSAbundVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->gobble(in);
- gobble(fileHandle);
+ }
+
+ }
+
+ in.close();
sabund = new SAbundVector();
*sabund = (input->getSAbundVector());
return sabund;
+
}
else{
- return 0;
+ 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";
+ m->errorOut(e, "InputData", "getSAbundVector");
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(){
+ 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);
+ }
+
+ m->gobble(fileHandle);
+
+ rabund = new RAbundVector();
+ *rabund = (input->getRAbundVector());
+
+ return rabund;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getRAbundVector");
exit(1);
- }
+ }
+}
+/***********************************************************************/
+RAbundVector* InputData::getRAbundVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->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; }
+ m->gobble(in);
+
+ }
+
+ }
+
+
+ in.close();
+
+ rabund = new RAbundVector();
+ *rabund = (input->getRAbundVector());
+
+ return rabund;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "InputData", "getRAbundVector");
+ exit(1);
+ }
}
/***********************************************************************/
+
+
+
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