1.21.0

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 9c56d2228092a25779cd0431c5a3a5ef06f81563..f1be7cbfbf3ef3d51c60234f2705a706d8697a06 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -179,21 +179,22 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { phylipfile = ""; abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  inputfile = phylipfile;  format = "phylip";     }
+                       else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);       }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { columnfile = ""; abort = true; }        
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  inputfile = columnfile; format = "column";      }
+                       else {  inputfile = columnfile; format = "column";      m->setColumnFile(columnfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  inputfile = sharedfile; format = "sharedfile";  }
+                       else {  inputfile = sharedfile; format = "sharedfile";  m->setSharedFile(sharedfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) { 
                                //is there are current file available for either of these?
@@ -408,7 +409,7 @@ int TreeGroupCommand::execute(){
                        //create tree file
                        makeSimsShared();
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
                }else{
                        //read in dist file
                        filename = inputfile;
@@ -563,7 +564,7 @@ int TreeGroupCommand::createTree(){
                //delete tree
                delete t;
                
-               if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+               if (m->control_pressed) { m->mothurRemove(outputFile); outputNames.pop_back(); return 1; }
                
                return 0;