changed heatmap and venn command to use vector of sharedrabunds instead of order...

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index c8259d90850c7d1c9f0ca0e2ba3a8f763e52f2e6..2c249e6a4a42b89a93b48a4252c60613f40fae9f 100644 (file)
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -10,6 +10,7 @@
 #include "inputdata.h"
 #include "ordervector.hpp"
 #include "listvector.hpp"
+#include "rabundvector.hpp"
 
 /***********************************************************************/
 
@@ -181,6 +182,39 @@ OrderVector* InputData::getOrderVector(){
                exit(1);
        }       
 }
+/***********************************************************************/
+
+vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
+       try {
+               if(fileHandle){
+                       if (format == "sharedfile")  {
+                               SharedOrder = new SharedOrderVector(fileHandle);
+                               if (SharedOrder != NULL) {
+                                       return SharedOrder->getSharedRAbundVector();
+                               }
+                       }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);
+       }       
+}
 
 /***********************************************************************/
 
@@ -225,3 +259,46 @@ 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);
+       }       
+}
+/***********************************************************************/
+
+
+