added path search for lookup file in shhh.seqs

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 9b0fcfd928cb5db6a6df12fb77a0583cc64cc4fb..16348c8d324a962ca336c82a2ad303f156cde9e3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -20,11 +20,11 @@ vector<string> ClusterCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);              
                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 pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
                CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
                CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -44,7 +44,7 @@ string ClusterCommand::getHelpString(){
                helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
                helpString += "The cluster command should be in the following format: \n";
                helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then furthest is assumed.\n\n";    
+               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -75,6 +75,7 @@ ClusterCommand::ClusterCommand(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();
@@ -149,10 +150,10 @@ ClusterCommand::ClusterCommand(string option)  {
                                //is there are current file available for either of these?
                                //give priority to column, then phylip
                                columnfile = m->getColumnFile(); 
-                               if (columnfile != "") {  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+                               if (columnfile != "") {  distfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
                                else { 
                                        phylipfile = m->getPhylipFile(); 
-                                       if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+                                       if (phylipfile != "") { distfile = phylipfile;  format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                        else { 
                                                m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the cluster command."); m->mothurOutEndLine(); 
                                                abort = true;
@@ -182,7 +183,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       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"; }
@@ -194,7 +195,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        cutoff += (5 / (precision * 10.0));  
                        
                        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")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }