altered venn command to make use of sharedchao for any number of groups, fixed window...

[mothur.git] / readseqscommand.h

diff --git a/readseqscommand.h b/readseqscommand.h
index 660eb3f37055ffe9d34f8c36c771ded2af327959..52c8a7c69615a432d48d40ebef60ff7acbab2eb2 100644 (file)
--- a/readseqscommand.h
+++ b/readseqscommand.h
@@ -5,7 +5,7 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 4/13/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -14,23 +14,6 @@
 #include "readnexus.h"
 #include "readclustal.h"
 #include "readseqsphylip.h"
-#include "inputdata.h"
-#include "groupmap.h"
-#include "sharedcommand.h"
-#include "parselistcommand.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;
 
@@ -46,9 +29,6 @@ private:
        ReadNexus* readNexus;
        ReadClustal* readClustal;
        ReadPhylip* readPhylip;
-       InputData* input;
-       Command* shared;
-       Command* parselist;
        string filename;
 };