working on current change

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index bdc8075342de2f484238c4810ee4da5babb0356c..9999eb0fb81e461e9f168c2c81b7531a3774607a 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -183,25 +183,27 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  distfile = phylipfile;  format = "phylip";      }
+                       else {  distfile = phylipfile;  format = "phylip";      m->setPhylipFile(phylipfile); }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       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 if (namefile == "not found") { namefile = "";  }
+                       else { m->setNameFile(namefile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }  
                        else if (fastafile == "not found") { fastafile = ""; }
-                       else { distfile = fastafile;  splitmethod = "fasta";  }
+                       else { distfile = fastafile;  splitmethod = "fasta";  m->setFastaFile(fastafile); }
                        
                        taxFile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxFile == "not open") { abort = true; }    
                        else if (taxFile == "not found") { taxFile = ""; }
+                       else {  m->setTaxonomyFile(taxFile); }
                        
                        if ((phylipfile == "") && (columnfile == "") && (fastafile == "")) { 
                                //is there are current file available for either of these?