added count file to cluster.classic and cluster.split. modified splitting classes...

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index a82d02270ecc37f1c85e93c9fe51b70e29288081..29dc69a05ad20ad7a19b7956fc3c55928ac5db35 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -15,7 +15,7 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 #include "readcluster.h"
 #include "splitmatrix.h"
 #include "readphylip.h"
@@ -35,6 +35,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "cluster.split";               }
        string getCommandCategory()             { return "Clustering";                  }
+       string getOutputFileNameTag(string, string);
        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"; }
@@ -46,7 +47,7 @@ private:
        vector<int> processIDS;   //processid
        vector<string> outputNames;
        
-       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
+       string 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;
@@ -61,6 +62,7 @@ private:
        int mergeLists(vector<string>, map<float, int>, ListVector*);
        map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
        int createMergedDistanceFile(vector< map<string, string> >);
+    int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund);
 };
 
 /////////////////not working for Windows////////////////////////////////////////////////////////////