X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sortseqscommand.h;h=c1de84e3876464a2216dbfaeeec3b153048ae34c;hp=b8078555385fe9f7d454366517c19d96238242f2;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=6f6cc4061459b264b0933111d90674ad7e4b0ecb

diff --git a/sortseqscommand.h b/sortseqscommand.h
index b807855..c1de84e 100644
--- a/sortseqscommand.h
+++ b/sortseqscommand.h
@@ -25,9 +25,11 @@ 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 or taxonomy file in the same order"; }
+    string getDescription()		{ return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
     
     int execute(); 
     void help() { m->mothurOut(getHelpString()); }	
@@ -35,15 +37,16 @@ public:
 	
 private:
     map<string, int> names;
-    string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, outputDir;
+    string accnosfile, fastafile, namefile, groupfile, countfile, taxfile, qualfile, flowfile, outputDir;
     bool abort, large;
     vector<string> outputNames;
     
     int readFasta();
+    int readFlow();
     int readName();
     int readGroup();
-    int readAccnos();
     int readTax();
+    int readCount();
     int readQual();
     
 };