added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 810b83915dadb9ed8863340dcfb27ac34e286dd8..ba59dfe66e1b333f88317542e3a17844ac6d558e 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -48,7 +48,7 @@ string SplitAbundCommand::getHelpString(){
                helpString += "If you want .abund and .rare files for all groups, set groups=all.  \n";
                helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
                helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -82,11 +82,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();