changes while testing

[mothur.git] / sortseqscommand.h

diff --git a/sortseqscommand.h b/sortseqscommand.h
index b8078555385fe9f7d454366517c19d96238242f2..c1de84e3876464a2216dbfaeeec3b153048ae34c 100644 (file)
--- 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();
     
 };