some alterations to chimera.slayer

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 2c31ba2245b523b7f18c0a3559ee9cd6f85890df..b8ab242e187b2f1b0fccc8b087e7c17f2cc0c903 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -16,9 +16,17 @@ class ScreenSeqsCommand : public Command {
        
 public:
        ScreenSeqsCommand(string);
-       ~ScreenSeqsCommand();
-       int execute();
-       void help();
+       ScreenSeqsCommand();
+       ~ScreenSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "screen.seqs";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
 
@@ -44,8 +52,15 @@ private:
 
        bool abort;
        string fastafile, namefile, groupfile, alignreport, outputDir;
-       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+       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 int>&);
+       int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+       int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);       
 };
 
 #endif