added kruskwalliscommand to Xcode project and fixed parameter issues.

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 2c6fec8d8d1082ea270f5e2c2a8832a7b57033a4..6149ef5b7ded364733fa4480dc9386d2e7e92fb2 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -15,6 +15,7 @@
 #include "chimera.h"
 #include "chimeraslayer.h"
 #include "sequenceparser.h"
+#include "sequencecountparser.h"
 
 /***********************************************************/
 
@@ -27,8 +28,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
+       
        string getHelpString(); 
-       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+    string getOutputPattern(string);   
+       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
@@ -50,12 +53,14 @@ private:
        int divideInHalf(Sequence, string&, string&);
        map<string, int> sortFastaFile(string, string);
        map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+    int sortFastaFile(vector<Sequence>&, map<string, int>&, string newFile);
        string getNamesFile(string&);
        //int setupChimera(string,);
        int MPIExecute(string, string, string, string, map<string, int>&);
-       int deconvoluteResults(SequenceParser*, string, string, string);
+       int deconvoluteResults(map<string, string>&, string, string, string);
        map<string, int> priority;
        int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+    int setUpForSelfReference(SequenceCountParser*&, map<string, string>&, map<string, map<string, int> >&, int);
        int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
        int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
        int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
@@ -65,8 +70,8 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
        #endif
 
-       bool abort, realign, trim, trimera, save;
-       string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
+       bool abort, realign, trim, trimera, save, hasName, hasCount;
+       string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;