working on current change

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index ce4b8950c3f1946054c7b24c82445a9ea1bc1cec..3e31691e6c8340d3ff7f02c0f316085f246f1b6b 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -203,6 +203,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") {                  
@@ -211,20 +212,22 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not found") { phylipfile = "";  }
                        else if (phylipfile == "not open") { abort = true; }    
-                       else { distFile = phylipfile; format = "phylip";   }
+                       else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);   }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not found") { columnfile = ""; }
                        else if (columnfile == "not open") { abort = true; }    
-                       else { distFile = columnfile; format = "column";   }
+                       else { distFile = columnfile; format = "column";  m->setColumnFile(columnfile); }
                        
                        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 == "")) { //is there are current file available for either of these?
                                //give priority to column, then phylip
@@ -263,7 +266,8 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
-                                               
+                       else { m->setGroupFile(groupfile); }
+                       
                        sorted = validParameter.validFile(parameters, "sorted", false);         if (sorted == "not found"){     sorted = "";    }
                        if (sorted == "none") { sorted=""; }
                        if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {