working on chimeras

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index bc87211e0bde9a4581119a91592683e34262d006..c39a638cf11375644a82e4d56c3c5659c56b35ee 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -18,7 +18,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","label","outputdir","inputdir"};
+                       string Array[] =  {"list","label","output","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -63,7 +63,11 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
                        else { 
                                splitAtDash(label, labels);
                                if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; }
-                       }                               
+                       }       
+                       
+                       output = validParameter.validFile(parameters, "output", false);                 if (output == "not found") { output = "name"; }
+                       
+                       if ((output != "name") && (output != "number")) { mothurOut("output options are name and number. I will use name."); mothurOutEndLine(); output = "name"; }
                }
                
        }
@@ -77,7 +81,8 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
 void OtuHierarchyCommand::help(){
        try {
                mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
-               mothurOut("The otu.hierarchy command parameters are list and label.  Both parameters are required. \n");
+               mothurOut("The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n");
+               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");
                mothurOut("The otu.hierarchy command should be in the following format: \n");
                mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
                mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
@@ -140,7 +145,8 @@ int OtuHierarchyCommand::execute(){
                        string names = lists[1].get(i);
                        
                        //output column 1
-                       out << names << '\t';
+                       if (output == "name")   {   out << names << '\t';       }
+                       else                                    {       out << i << '\t';               }
                        
                        map<int, int> bins; //bin numbers in little that are in this bin in big
                        map<int, int>::iterator it;
@@ -157,7 +163,8 @@ int OtuHierarchyCommand::execute(){
                        
                        string col2 = "";
                        for (it = bins.begin(); it != bins.end(); it++) {
-                               col2 += lists[0].get(it->first) + "\t";
+                               if (output == "name")   {   col2 += lists[0].get(it->first) + "\t";     }
+                               else                                    {       col2 += toString(it->first) + "\t";             }
                        }
                        
                        //output column 2