X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sortseqscommand.h;h=4ba8e4294d4b7d01bc8de7ba57cef84817f718ce;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=0685d3bad74dde206fce4872fd165186f15df355;hpb=731d19a6eaf81768ed35e4be25fbac5686a2a7a0;p=mothur.git

diff --git a/sortseqscommand.h b/sortseqscommand.h
index 0685d3b..4ba8e42 100644
--- a/sortseqscommand.h
+++ b/sortseqscommand.h
@@ -25,7 +25,8 @@ public:
     vector<string> setParameters();
     string getCommandName()			{ return "sort.seqs";				}
     string getCommandCategory()		{ return "Sequence Processing";		}
-    string getHelpString();	
+    string getOutputFileNameTag(string, string);
+	string getHelpString();	
     string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
     string getDescription()		{ return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
     
@@ -35,7 +36,7 @@ public:
 	
 private:
     map<string, int> names;
-    string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, flowfile, outputDir;
+    string accnosfile, fastafile, namefile, groupfile, countfile, taxfile, qualfile, flowfile, outputDir;
     bool abort, large;
     vector<string> outputNames;
     
@@ -43,8 +44,8 @@ private:
     int readFlow();
     int readName();
     int readGroup();
-    int readAccnos();
     int readTax();
+    int readCount();
     int readQual();
     
 };