broke up globaldata and moved error checking and help into commands

[mothur.git] / readotu.cpp

diff --git a/readotu.cpp b/readotu.cpp
index 455641a8f52b7cb24c0b5e74d19ff83c27ed6667..09a6c4cd00f58d5fc09424972c3f6ae93c88542d 100644 (file)
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -20,6 +20,7 @@ ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
 //This function reads the list, rabund or sabund files to be used by collect and rarefact command.
 void ReadOTUFile::read(GlobalData* globaldata){
        try {
+
                if (globaldata->getOrderFile() == "") {
                        //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.
@@ -46,6 +47,7 @@ void ReadOTUFile::read(GlobalData* globaldata){
                        globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
                        list = inputList->getListVector();
                        globaldata->gListVector = list;
+
                }else if (globaldata->getFormat() == "shared") {
                        SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
                        //memory leak prevention