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

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 2d26ef3672a364cd694e01d48922d9d53e56b0db..6e4082e0c139b76435aa073cd1f0c7013b85dca3 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -10,50 +10,51 @@
 #include "parselistscommand.h"
 
 //**********************************************************************************************************************
-vector<string> ParseListCommand::getValidParameters(){ 
+vector<string> ParseListCommand::setParameters(){      
        try {
-               string Array[] =  {"list","group", "label", "outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+               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, "ParseListCommand", "getValidParameters");
+               m->errorOut(e, "ParseListCommand", "setParameters");
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
-ParseListCommand::ParseListCommand(){  
+string ParseListCommand::getHelpString(){      
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["list"] = tempOutNames;
+               string helpString = "";
+               helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n";
+               helpString += "The parse.list command parameters are list, group and label.\n";
+               helpString += "The list and group parameters are required.\n";
+               helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
+               helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
+               helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ParseListCommand", "ParseListCommand");
+               m->errorOut(e, "ParseListCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ParseListCommand::getRequiredParameters(){      
-       try {
-               string Array[] =  {"list","group"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ParseListCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ParseListCommand::getRequiredFiles(){   
+ParseListCommand::ParseListCommand(){  
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "ParseListCommand", "getRequiredFiles");
+               m->errorOut(e, "ParseListCommand", "ParseListCommand");
                exit(1);
        }
 }
@@ -67,9 +68,7 @@ ParseListCommand::ParseListCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"list","group", "label", "outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
@@ -115,12 +114,28 @@ ParseListCommand::ParseListCommand(string option)  {
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
-                       else if (listfile == "not found") { listfile = ""; }    
+                       else if (listfile == "not found") { 
+                               listfile = m->getListFile(); 
+                               if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+                               else { 
+                                       m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
+                                       abort = true;
+                                               
+                               }
+                       }       
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
-                       else if (groupfile == "not found") { groupfile = ""; }
-                       else {  
+                       else if (groupfile == "not found") { 
+                               groupfile = m->getListFile(); 
+                               if (groupfile != "") {  
+                                       m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); 
+                                       groupMap = new GroupMap(groupfile);
+                                       
+                                       int error = groupMap->readMap();
+                                       if (error == 1) { abort = true; }
+                               }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
+                       }else {  
                                groupMap = new GroupMap(groupfile);
                                
                                int error = groupMap->readMap();
@@ -147,25 +162,6 @@ ParseListCommand::ParseListCommand(string option)  {
        }
 }
 //**********************************************************************************************************************
-void ParseListCommand::help(){
-       try {
-               m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n");
-               m->mothurOut("The parse.list command parameters are list, group and label.\n");
-               m->mothurOut("The list and group parameters are required.\n");
-               m->mothurOut("The label parameter is used to read specific labels in your input you want to use.\n");
-               m->mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n");
-               m->mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
-
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ParseListCommand", "help");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-ParseListCommand::~ParseListCommand(){}
-//**********************************************************************************************************************
 int ParseListCommand::execute(){
        try {