added dereplicate parameter to chimera.slayer and chimera.persues. added minnumsample...

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 291d8e6d1acd4605f4827159f10aa74269e1a771..284c9a5ac1a0bd5c90dca6b4854b725d6b428023 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,7 +23,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "screen.seqs";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
        string getDescription()         { return "enables you to keep sequences that fulfill certain user defined criteria"; }
 
@@ -43,6 +45,7 @@ private:
 
        int screenNameGroupFile(set<string>);
        int screenGroupFile(set<string>);
+    int screenCountFile(set<string>);
        int screenAlignReport(set<string>);
        int screenQual(set<string>);
        int screenTaxonomy(set<string>);
@@ -55,12 +58,11 @@ private:
        #endif
 
        bool abort;
-       string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+       string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile;
        int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
        vector<string> outputNames;
        vector<string> optimize;
        map<string, int> nameMap;
-       int readNames();
        
        int getSummary(vector<unsigned long long>&);
        int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);