removed line option

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 6ec35412c3c82206bef933787c820ca36e2158d2..dd0cf3adab7798c71e9e853ff1e5b33c8f53a690 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -15,19 +15,6 @@
 #include "groupmap.h"
 #include "sharedcommand.h"
 
-/* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single, 
-collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund 
-upon completion of the cluster command or you may use your own. The read.otu command parameter options are 
-listfile, rabundfile, sabundfile, groupfile and orderfile. The reaad.otu command can be used in two ways. 
-The first is to read a listfile, rabundfile or sabundfile and run the collect.single, rarefaction.single or summary.single. 
-For this use the read.otu command should be in the following format: read.otu(listfile=yourListFile, orderfile=yourOrderFile). 
-The listfile, rabundfile or sabundfile parameter is required, but you may only use one of them. 
-The second way to use the read.otu command is to read a listfile and a groupfile so you can use the collect.shared, 
-rarefaction.shared or summary.shared commands. In this case the read.otu command should be in the following format: 
-read.otu(listfile=yourListFile, groupfile=yourGroupFile). The listfile parameter and groupfile paramaters are required. 
-When using the command the second way read.otu command parses the .list file and separates it into groups. 
-It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. */
-
 class GlobalData;
 
 class ReadOtuCommand : public Command {
@@ -39,14 +26,12 @@ public:
        
 private:
        GlobalData* globaldata;
-       //ReadOTUFile* read;
        InputData* input;
        Command* shared;
        GroupMap* groupMap;
-       string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+       string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format;
 
        bool abort, allLines;
-       set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
 
 };