fixing minor bugs

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index 4ed9c2711d2f11b0182ec165884d3747eeb0be80..b237bb4fc55b0bacafa3815f9619f0345bd31492 100644 (file)
--- 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);
+       }       
+}
+/***********************************************************************/
+
+
+