working on current change

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index fc173100942199c9f5f5ea1b400d0cb0ad978303..0d836130d31124298a13c3a388267144cf5538ff 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -169,15 +169,18 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        //check for required parameters                 
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -186,6 +189,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
@@ -193,7 +197,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                                taxfile = m->getTaxonomyFile(); 
                                if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setTaxonomyFile(taxfile); }
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);