added ability for user to select which groups to analyze with the collect.shared...

[mothur.git] / readmatrix.cpp

diff --git a/readmatrix.cpp b/readmatrix.cpp
index bd92f6c40ef1638ece9fe6319651fff48be83fa3..2d981243518004bccb81a0779762b824cf20f4c7 100644 (file)
--- a/readmatrix.cpp
+++ b/readmatrix.cpp
@@ -9,15 +9,11 @@
 
 using namespace std;
 
-#include <string>
-#include <map>
 #include "utilities.hpp"
 #include "sparsematrix.hpp"
 #include "progress.hpp"
 #include "listvector.hpp"
 #include "rabundvector.hpp"
-#include <exception>
-
 #include "readmatrix.hpp"
 
 
@@ -346,19 +342,19 @@ void ReadPhilFile::read(GlobalData* globaldata){
                        //you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.  
                        //So when you run the collect or summary commands you miss a line.
                        input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
-                       inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
+                       inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
                }else {//there is an orderfile
                        input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
                }
                globaldata->ginput = input;     //saving to be used by collector and rarefact commands.
                
-               if (globaldata->getGroupFile() == "") {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
+               if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
                        order = input->getOrderVector();
                        globaldata->gorder = order;     //saving to be used by collect and rarefact commands.
                        sabund = inputSabund->getSAbundVector(); 
                        globaldata->sabund = sabund; //saving to be used by summary command.
-               }else {
-                       SharedList = input->getSharedListVector(); //you are reading for parselist command, or shared commands.
+               }else if (globaldata->getFormat() == "shared") {
+                       SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
                        globaldata->gSharedList = SharedList;
                }
        }