added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index cf52ff27d01c28d61f90aa0a8c514d4a04b2136d..a82d02270ecc37f1c85e93c9fe51b70e29288081 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -23,6 +23,7 @@
 #include "readmatrix.hpp"
 #include "inputdata.h"
 #include "clustercommand.h"
+#include "clusterclassic.h"
 
 class ClusterSplitCommand : public Command {
        
@@ -48,13 +49,15 @@ private:
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
-       bool print_start, abort, hard, large;
+       bool print_start, abort, hard, large, classic;
        time_t start;
        ofstream outList, outRabund, outSabund;
        
        void printData(ListVector*);
        vector<string> createProcesses(vector< map<string, string> >, set<string>&);
        vector<string> cluster(vector< map<string, string> >, set<string>&);
+    string clusterFile(string, string, set<string>&, double&);
+    string clusterClassicFile(string, string, set<string>&, double&);
        int mergeLists(vector<string>, map<float, int>, ListVector*);
        map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
        int createMergedDistanceFile(vector< map<string, string> >);
@@ -102,7 +105,7 @@ struct clusterData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){ 
        clusterData* pDataArray;