indicator command

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 810b83915dadb9ed8863340dcfb27ac34e286dd8..aa47940a030f968e02686b915d26e84c29584b8d 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();
@@ -154,12 +152,12 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else{ inputFile = listfile; }   
+                       else{ inputFile = listfile; m->setListFile(listfile); } 
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-                       else{ inputFile = namefile; }   
+                       else{ inputFile = namefile; m->setNameFile(namefile); } 
                
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -167,7 +165,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
@@ -177,7 +175,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                
                                int error = groupMap->readMap();
                                if (error == 1) { abort = true; }
-       
+                               m->setGroupFile(groupfile);
                        }
                        
                        groups = validParameter.validFile(parameters, "groups", false);