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

[mothur.git] / splitgroupscommand.cpp

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 16d90a48372f7c97d46f7fd4d0b640fde6b533fb..bdb6e7c0151b10cb96fc6d0aa59d66199dba2e6f 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -11,37 +11,41 @@
 #include "sharedutilities.h"
 
 //**********************************************************************************************************************
-vector<string> SplitGroupCommand::getValidParameters(){        
-       try {
-               string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"}; 
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+vector<string> SplitGroupCommand::setParameters(){     
+       try {           
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+               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, "SplitGroupCommand", "getValidParameters");
+               m->errorOut(e, "SplitGroupCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredParameters(){     
+string SplitGroupCommand::getHelpString(){     
        try {
-               string Array[] =  {"fasta","group"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The split.group command reads a group file, and parses your fasta and names files by groups. \n";
+               helpString += "The split.group command parameters are fasta, name, group and groups.\n";
+               helpString += "The fasta and group parameters are required.\n";
+               helpString += "The groups parameter allows you to select groups to create files for.  \n";
+               helpString += "For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files.  \n";
+               helpString += "If you want .fasta and .names files for all groups, set groups=all.  \n";
+               helpString += "The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n";
+               helpString += "Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\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, "SplitGroupCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredFiles(){  
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
+               m->errorOut(e, "SplitGroupCommand", "getHelpString");
                exit(1);
        }
 }
@@ -49,6 +53,7 @@ vector<string> SplitGroupCommand::getRequiredFiles(){
 SplitGroupCommand::SplitGroupCommand(){        
        try {
                abort = true; calledHelp = true; 
+               setParameters();
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
@@ -67,9 +72,7 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"}; 
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
@@ -125,11 +128,19 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                
                        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 split.group 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; }
+                       }       
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
-                       else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the split.group command. "); m->mothurOutEndLine(); abort = true; }
+                       else if (groupfile == "not found") {                    
+                               groupfile = m->getGroupFile(); 
+                               if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }
                        
                        groups = validParameter.validFile(parameters, "groups", false);         
                        if (groups == "not found") { groups = ""; }
@@ -146,27 +157,6 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
        }
 }
 //**********************************************************************************************************************
-void SplitGroupCommand::help(){
-       try {
-               m->mothurOut("The split.group command reads a group file, and parses your fasta and names files by groups. \n");
-               m->mothurOut("The split.group command parameters are fasta, name, group and groups.\n");
-               m->mothurOut("The fasta and group parameters are required.\n");
-               m->mothurOut("The groups parameter allows you to select groups to create files for.  \n");
-               m->mothurOut("For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files.  \n");
-               m->mothurOut("If you want .fasta and .names files for all groups, set groups=all.  \n");
-               m->mothurOut("The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n");
-               m->mothurOut("Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\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, "SplitGroupCommand", "help");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-SplitGroupCommand::~SplitGroupCommand(){ }
-//**********************************************************************************************************************
 int SplitGroupCommand::execute(){
        try {