changes while testing

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index d2b2e03a3196d61cf7036ff879f1a18bec741ae6..fa195e7253e870f2a38b8e72ca90a1a6875e4652 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
-
+#include "referencedb.h"
 
 /***********************************************************/
 
@@ -23,20 +23,26 @@ public:
 
        ChimeraPintailCommand(string);
        ChimeraPintailCommand();
-       ~ChimeraPintailCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ChimeraPintailCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.pintail";             }
+       string getCommandCategory()             { return "Sequence Processing"; }
        
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
-
+       ReferenceDB* rdb;
+       
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
 
        vector<int> processIDS;   //processid
@@ -46,18 +52,15 @@ private:
        int createProcesses(string, string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, filter;
+       bool abort, filter, save;
        string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
-       
-       
 };
 
 /***********************************************************/