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

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 5bcfe03416f90700a02a4ff3d58ad312f788bb96..a9d3214b1d7ffb793d8a7813a55f26b7824795a0 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -11,51 +11,55 @@
 #include "clusterclassic.h"
 
 //**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getValidParameters(){      
+vector<string> ClusterDoturCommand::setParameters(){   
        try {
-               string AlignArray[] =  {"phylip","name","hard","cutoff","precision","method","outputdir","inputdir"};
-               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
+               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, "ClusterDoturCommand", "getValidParameters");
+               m->errorOut(e, "ClusterDoturCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-ClusterDoturCommand::ClusterDoturCommand(){    
+string ClusterDoturCommand::getHelpString(){   
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["list"] = tempOutNames;
-               outputTypes["rabund"] = tempOutNames;
-               outputTypes["sabund"] = tempOutNames;
+               string helpString = "";
+               helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
+               helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
+               helpString += "The cluster.classic command should be in the following format: \n";
+               helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
+               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then furthest is assumed.\n\n";    
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
+               m->errorOut(e, "ClusterDoturCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getRequiredParameters(){   
-       try {
-               string Array[] =  {"phylip"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClusterDoturCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getRequiredFiles(){        
+ClusterDoturCommand::ClusterDoturCommand(){    
        try {
-               vector<string> myArray; 
-               return myArray;
+               abort = true; calledHelp = true;
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "ClusterDoturCommand", "getRequiredFiles");
+               m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
                exit(1);
        }
 }
@@ -70,9 +74,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"phylip","name","cutoff","hard","precision","method","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -122,7 +124,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        //check for required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
-                       else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("When executing the cluster.dotur command you must enter a phylip file."); m->mothurOutEndLine(); abort = true; }   
+                       else if (phylipfile == "not found") { 
+                               phylipfile = m->getPhylipFile(); 
+                               if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+                               else { 
+                                       m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine(); 
+                                       abort = true; 
+                               }       
+                       }       
 
                
                        //check for optional parameter and set defaults
@@ -145,6 +154,9 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
                        hard = m->isTrue(temp);
                        
+                       temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
+                       sim = m->isTrue(temp); 
+                       
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
                        
@@ -161,28 +173,6 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-void ClusterDoturCommand::help(){
-       try {
-               m->mothurOut("The cluster.classic command clusters using the algorithm from dotur. \n");
-               m->mothurOut("The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, precision. Phylip is required.\n");
-               m->mothurOut("The cluster.classic command should be in the following format: \n");
-               m->mothurOut("cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               m->mothurOut("The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then furthest is assumed.\n\n");    
-
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClusterDoturCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-ClusterDoturCommand::~ClusterDoturCommand(){}
-
 //**********************************************************************************************************************
 
 int ClusterDoturCommand::execute(){
@@ -198,7 +188,7 @@ int ClusterDoturCommand::execute(){
                }
                
                //reads phylip file storing data in 2D vector, also fills list and rabund
-               ClusterClassic* cluster = new ClusterClassic(cutoff, method);
+               ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
                cluster->readPhylipFile(phylipfile, nameMap);
                
                if (m->control_pressed) { delete cluster; delete list; delete rabund; return 0; }