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

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index b49af32a76c1cbb2d65ab2a5bf32555a171c5de7..17e29d9528c1122f73a2f81a32c1998dded037cf 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -10,49 +10,53 @@
 #include "otuhierarchycommand.h"
 
 //**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getValidParameters(){      
+vector<string> OtuHierarchyCommand::setParameters(){   
        try {
-               string Array[] =  {"list","label","output","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+               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, "OtuHierarchyCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(){    
-       try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["otuheirarchy"] = tempOutNames;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+               m->errorOut(e, "OtuHierarchyCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getRequiredParameters(){   
+string OtuHierarchyCommand::getHelpString(){   
        try {
-               string Array[] =  {"list","label"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n";
+               helpString += "The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n";
+               helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n";
+               helpString += "The otu.hierarchy command should be in the following format: \n";
+               helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
+               helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
+               helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\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, "OtuHierarchyCommand", "getRequiredParameters");
+               m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getRequiredFiles(){        
+OtuHierarchyCommand::OtuHierarchyCommand(){    
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["otuheirarchy"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles");
+               m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
                exit(1);
        }
 }
@@ -65,9 +69,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                if(option == "help") {  help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"list","label","output","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -99,8 +101,14 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                        }
 
                        listFile = validParameter.validFile(parameters, "list", true);
-                       if (listFile == "not found") { m->mothurOut("list is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
-                       else if (listFile == "not open") { abort = true; }      
+                       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;
+                               }
+                       }else if (listFile == "not open") { 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"){  
@@ -130,29 +138,6 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 }
 //**********************************************************************************************************************
 
-void OtuHierarchyCommand::help(){
-       try {
-               m->mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
-               m->mothurOut("The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n");
-               m->mothurOut("The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n");
-               m->mothurOut("The otu.hierarchy command should be in the following format: \n");
-               m->mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
-               m->mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
-               m->mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\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, "OtuHierarchyCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-OtuHierarchyCommand::~OtuHierarchyCommand(){}
-
-//**********************************************************************************************************************
-
 int OtuHierarchyCommand::execute(){
        try {