rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index a9d3214b1d7ffb793d8a7813a55f26b7824795a0..0d57e68a8a0b656798e107dd7f69eea6d7b9205c 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -17,8 +17,8 @@ vector<string> ClusterDoturCommand::setParameters(){
                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 pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",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);
@@ -40,7 +40,7 @@ string ClusterDoturCommand::getHelpString(){
                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";    
+               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -72,6 +72,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -131,13 +132,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                                        m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine(); 
                                        abort = true; 
                                }       
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
 
                
                        //check for optional parameter and set defaults
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);
@@ -151,14 +153,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        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"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { 
                                if (method == "furthest") { tag = "fn"; }
@@ -217,7 +219,7 @@ int ClusterDoturCommand::execute(){
                int estart = time(NULL);
        
                while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
-                       if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());         } outputTypes.clear();  return 0;  }
+                       if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } outputTypes.clear();  return 0;  }
                
                        cluster->update(cutoff);