X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=9bce0995ee9cc9d7f212df0296335487502a3fd9;hb=f6c7165727bc17a5fbbcbb774d75ccffeb7f3da5;hp=631a8b6c8b95bfa87c52035cdb91d53bc7b378aa;hpb=47faf5463d44570ad66148384763db1c8238b563;p=mothur.git

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 631a8b6..9bce099 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -23,7 +23,12 @@ class ClusterSplitCommand : public Command {
 	
 public:
 	ClusterSplitCommand(string);
+	ClusterSplitCommand();
 	~ClusterSplitCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
@@ -31,18 +36,21 @@ private:
 	GlobalData* globaldata;
 	vector<int> processIDS;   //processid
 	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 
-	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
 	double cutoff, splitcutoff;
-	int precision, length, processors;
-	bool print_start, abort, hard;
+	int precision, length, processors, taxLevelCutoff;
+	bool print_start, abort, hard, large;
 	time_t start;
 	ofstream outList, outRabund, outSabund;
 	
 	void printData(ListVector*);
 	int createProcesses(vector < vector < map<string, string> > >);
 	vector<string> cluster(vector< map<string, string> >, set<string>&);
-	int mergeLists(vector<string>, string, set<string>);
+	int mergeLists(vector<string>, map<float, int>, ListVector*);
+	map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
+	int createMergedDistanceFile(vector< map<string, string> >);
 };
 
 #endif