removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index a8a9d2b5a6cff6da2ab8e86e22af19782f5ce0bf..b977304c9ce54493e5f34dc20705ea1855b21bc4 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -11,50 +11,55 @@
 #include "sequence.hpp"
 #include "listvector.hpp"
 
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getValidParameters(){  
+vector<string> ListSeqsCommand::setParameters(){       
        try {
-               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+               CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "getValidParameters");
+               m->errorOut(e, "ListSeqsCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-ListSeqsCommand::ListSeqsCommand(){    
+string ListSeqsCommand::getHelpString(){       
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["accnos"] = tempOutNames;
+               string helpString = "";
+               helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+               helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n";
+               helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+               helpString += "Example list.seqs(fasta=amazon.fasta).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredParameters(){       
-       try {
-               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","or"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+               m->errorOut(e, "ListSeqsCommand", "getHelpString");
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredFiles(){    
+ListSeqsCommand::ListSeqsCommand(){    
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
                exit(1);
        }
 }
@@ -68,9 +73,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -186,22 +189,6 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void ListSeqsCommand::help(){
-       try {
-               m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
-               m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n");
-               m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
-               m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
 int ListSeqsCommand::execute(){
        try {