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

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 1d87204abd165396a20f99cbef0e3440eadbcd95..fb02764e93cc8ca2494773aebeccab857e58f378 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -11,49 +11,49 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-vector<string> DeUniqueSeqsCommand::getValidParameters(){      
+vector<string> DeUniqueSeqsCommand::setParameters(){   
        try {
-               string Array[] =  {"fasta", "name","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+               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, "DeUniqueSeqsCommand", "getValidParameters");
+               m->errorOut(e, "DeUniqueSeqsCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
+string DeUniqueSeqsCommand::getHelpString(){   
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["fasta"] = tempOutNames;
+               string helpString = "";
+               helpString += "The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n";
+               helpString += "The deunique.seqs command parameters are fasta and name, both are required, unless you have valid current name and fasta files.\n";
+               helpString += "The deunique.seqs command should be in the following format: \n";
+               helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n";       
+               helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\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, "DeUniqueSeqsCommand", "DeconvoluteCommand");
+               m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> DeUniqueSeqsCommand::getRequiredParameters(){   
-       try {
-               string Array[] =  {"fasta","name"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> DeUniqueSeqsCommand::getRequiredFiles(){        
+DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredFiles");
+               m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand");
                exit(1);
        }
 }
@@ -66,9 +66,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta", "name","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -111,7 +109,11 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                        //check for required parameters
                        fastaFile = validParameter.validFile(parameters, "fasta", true);
                        if (fastaFile == "not open") { abort = true; }
-                       else if (fastaFile == "not found") { fastaFile = ""; m->mothurOut("fasta is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true;  }      
+                       else if (fastaFile == "not found") {                            
+                               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; }
+                       }       
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -121,7 +123,11 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                        
                        nameFile = validParameter.validFile(parameters, "name", true);
                        if (nameFile == "not open") { abort = true; }
-                       else if (nameFile == "not found"){      nameFile = "";  m->mothurOut("name is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true;  }
+                       else if (nameFile == "not found"){                                      
+                               nameFile = m->getNameFile(); 
+                               if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }
                }
 
        }
@@ -130,24 +136,6 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void DeUniqueSeqsCommand::help(){
-       try {
-               m->mothurOut("The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n");
-               m->mothurOut("The deunique.seqs command parameters are fasta and name, both are required.\n");
-               m->mothurOut("The deunique.seqs command should be in the following format: \n");
-               m->mothurOut("deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n");       
-               m->mothurOut("Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\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, "DeUniqueSeqsCommand", "help");
-               exit(1);
-       }
-}
-
 /**************************************************************************************/
 int DeUniqueSeqsCommand::execute() {   
        try {