working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index b37d4c04ac397fb2ede7ba1d2e0501b9508e5b9d..54b8fa182894fd448dff3e5a7b6548532334b258 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,6 +14,7 @@
 #include "command.hpp"
 #include "chimera.h"
 #include "chimeraslayer.h"
+#include "sequenceparser.h"
 
 /***********************************************************/
 
@@ -43,19 +44,25 @@ private:
 
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
-       map<string, int> priority;
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
        int divideInHalf(Sequence, string&, string&);
        map<string, int> sortFastaFile(string, string);
+       map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+       string getNamesFile(string&);
+       int setupChimera(string, map<string, int>&);
+       int MPIExecute(string, string, string, string);
+       int deconvoluteResults(SequenceParser*, string, string, string);
+       map<string, int> priority;
+
                
        #ifdef USE_MPI
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
        bool abort, realign, trim, trimera, save;
-       string fastafile, templatefile, outputDir, search, namefile, blastlocation;
+       string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;
@@ -63,6 +70,7 @@ private:
        vector<string> outputNames;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
+       vector<string> groupFileNames;
        
 };
 
@@ -71,7 +79,7 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct slayerData {
+struct slayerData {
        string outputFName; 
        string fasta; 
        string accnos;