1.22.0

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 9ed887a72ff7354c9396ba2d2c63f3b4a460afd3..9742bcbd3b0ea952e3a5b5b54428bee701c5191f 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -232,10 +232,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        if ((phylipfile == "") && (columnfile == "")) { //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 get.oturep command."); m->mothurOutEndLine(); 
                                                abort = true;
@@ -290,7 +290,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                        m->splitAtDash(groups, Groups);
                                }
                        }
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        string temp = validParameter.validFile(parameters, "large", false);             if (temp == "not found") {      temp = "F";     }
                        large = m->isTrue(temp);
@@ -429,7 +429,9 @@ int GetOTURepCommand::execute(){
                        
                        if (Groups.size() != 0) {
                                SharedUtil* util = new SharedUtil();
-                               util->setGroups(Groups, groupMap->namesOfGroups, "getoturep");
+                               vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+                               util->setGroups(Groups, gNamesOfGroups, "getoturep");
+                               groupMap->setNamesOfGroups(gNamesOfGroups);
                                delete util;
                        }
                }