added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index dc46f9904a594919d3789c4c98f06ec7a7c159d7..c4b236cb12dbfc535c1de5da7840b39f21176fb7 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -16,22 +16,29 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
-#include "globaldata.hpp"
 
 
 class ClusterSplitCommand : public Command {
        
 public:
        ClusterSplitCommand(string);
-       ~ClusterSplitCommand();
-       int execute();  
-       void help();
+       ClusterSplitCommand();
+       ~ClusterSplitCommand() {}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "cluster.split";               }
+       string getCommandCategory()             { return "Clustering";                  }
+       string getHelpString(); 
+       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. \nhttp://www.mothur.org/wiki/Cluster.split"; }
+       string getDescription()         { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+
 private:
-       GlobalData* globaldata;
        vector<int> processIDS;   //processid
        vector<string> outputNames;
-
+       
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
@@ -44,6 +51,7 @@ private:
        vector<string> cluster(vector< map<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