indicator command

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 323dd45a5690cd047742b16b9bdb9f9c08972a5a..9172819bd78f39dfee97b94c4c4b24c79bd080ae 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -139,15 +139,17 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        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); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = "";  }   
+                       else { m->setListFile(listfile); }
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
@@ -536,7 +538,6 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
                        if (counts[i] < zeroCutoff) { counts[i] = 0; }
                }
                
-               
                //any
                if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'n'; }
                //any no gap
@@ -600,7 +601,7 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
                //only gap
                else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = '-'; }
                //cutoff removed all counts
-               else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  m->mothurOut("cutoff ...."); m->mothurOutEndLine(); }
+               else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'N'; }
                else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
                
                return conBase;