fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index b4e41e5fb60f48823528907df5804ff05c01c419..c2be580bb73313c91322e903c87027dc5da405d9 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -168,12 +168,12 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        
                        //check for required parameters                 
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not open") { abort = true; }
+                       if (fastafile == "not open") { fastafile = ""; abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }
                        else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
                        else { m->setNameFile(namefile); }
                        
@@ -192,7 +192,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
-                       if (taxfile == "not open") { abort = true; }
+                       if (taxfile == "not open") { taxfile = ""; abort = true; }
                        else if (taxfile == "not found") {                              
                                taxfile = m->getTaxonomyFile(); 
                                if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
@@ -217,6 +217,11 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        m->splitAtChar(taxons, listOfTaxons, '-');
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
+               
+                       if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+                               vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+                               parser.getNameFile(files);
+                       }
                }
 
        }