added read.shared, broke up globaldata a bit

[mothur.git] / readmatrix.cpp

diff --git a/readmatrix.cpp b/readmatrix.cpp
index 78a4bd4efe97b355513c51bec77616cbefa6a4e7..72dd799ec6d2e419dd843db6288de313fa0b4078 100644 (file)
--- a/readmatrix.cpp
+++ b/readmatrix.cpp
@@ -346,7 +346,7 @@ 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());
                }
@@ -358,7 +358,7 @@ void ReadPhilFile::read(GlobalData* globaldata){
                        sabund = inputSabund->getSAbundVector(); 
                        globaldata->sabund = sabund; //saving to be used by summary command.
                }else if (globaldata->getFormat() == "shared") {
-                       SharedList = input->getSharedListVector(); //you are reading for parselist command, or shared commands.
+                       SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
                        globaldata->gSharedList = SharedList;
                }
        }