X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=2e8ac6356787aa90bcde2ac88155e3064a6e4da2;hb=aca78ed4a47dff8672ea8fd93cef0dfbaf0f7495;hp=936ae6f69ce94877b60b9f99219423db8b526d73;hpb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;p=mothur.git

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 936ae6f..2e8ac63 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -35,8 +35,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.split";		}
 	string getCommandCategory()		{ return "Clustering";			}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
 	string getDescription()		{ return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
 	
@@ -47,10 +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;
+	bool print_start, abort, hard, large, classic, runCluster, deleteFiles;
 	time_t start;
 	ofstream outList, outRabund, outSabund;
 	
@@ -63,6 +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////////////////////////////////////////////////////////////