added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 0e32ffaea7710189859f458de4adc897362e12ef..28de9488b68516e2e194db0dd35920c7078e91f9 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -23,6 +23,7 @@
 #include "readmatrix.hpp"
 #include "inputdata.h"
 #include "clustercommand.h"
+#include "clusterclassic.h"
 
 class ClusterSplitCommand : public Command {
        
@@ -34,6 +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"; }
@@ -48,13 +50,15 @@ private:
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
-       bool print_start, abort, hard, large;
+       bool print_start, abort, hard, large, classic;
        time_t start;
        ofstream outList, outRabund, outSabund;
        
        void printData(ListVector*);
        vector<string> createProcesses(vector< map<string, string> >, set<string>&);
        vector<string> cluster(vector< map<string, string> >, set<string>&);
+    string clusterFile(string, string, set<string>&, double&);
+    string clusterClassicFile(string, string, set<string>&, double&);
        int mergeLists(vector<string>, map<float, int>, ListVector*);
        map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
        int createMergedDistanceFile(vector< map<string, string> >);