working on sra and get.mimarkspackage commands. added file parameter to cluster...

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index e1f17b1bd0b8c4088d5deb3c06691fb3ccf26999..2e8ac6356787aa90bcde2ac88155e3064a6e4da2 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -48,10 +48,10 @@ private:
        vector<int> processIDS;   //processid
        vector<string> outputNames;
        
-       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
+       string file, method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
-       bool print_start, abort, hard, large, classic, runCluster;
+       bool print_start, abort, hard, large, classic, runCluster, deleteFiles;
        time_t start;
        ofstream outList, outRabund, outSabund;
        
@@ -64,6 +64,8 @@ private:
        map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
        int createMergedDistanceFile(vector< map<string, string> >);
     int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund);
+    string readFile(vector< map<string, string> >&);
+    int printFile(string, vector< map<string, string> >&);
 };
 
 /////////////////not working for Windows////////////////////////////////////////////////////////////