X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sortseqscommand.h;h=c1de84e3876464a2216dbfaeeec3b153048ae34c;hp=0685d3bad74dde206fce4872fd165186f15df355;hb=615301e57c25e241356a9c2380648d117709458d;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/sortseqscommand.h b/sortseqscommand.h
index 0685d3b..c1de84e 100644
--- a/sortseqscommand.h
+++ b/sortseqscommand.h
@@ -25,7 +25,9 @@ public:
     vector<string> setParameters();
     string getCommandName()			{ return "sort.seqs";				}
     string getCommandCategory()		{ return "Sequence Processing";		}
-    string getHelpString();	
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
     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 +37,7 @@ 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 +45,8 @@ private:
     int readFlow();
     int readName();
     int readGroup();
-    int readAccnos();
     int readTax();
+    int readCount();
     int readQual();
     
 };