changing command name classify.shared to classifyrf.shared

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 59039ea8600a4ac7e4ea30ab2a684679f6c9f51e..e1f17b1bd0b8c4088d5deb3c06691fb3ccf26999 100644 (file)
--- 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, 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;
+       bool print_start, abort, hard, large, classic, runCluster;
        time_t start;
        ofstream outList, outRabund, outSabund;
        
@@ -62,6 +63,7 @@ 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////////////////////////////////////////////////////////////
@@ -75,7 +77,7 @@ private:
 // anything to do with mothur's use of copy constructors in many of our data structures. ie. listvector 
 // is copied by nameassignment and passed to read which passes to the thread?  -westcott 2-8-12
 ////////////////////////////////////////////////////////////////////////////////////////////////////
-/**************************************************************************************************/
+/**************************************************************************************************
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
@@ -105,7 +107,7 @@ struct clusterData {
        }
 };
 
-/**************************************************************************************************/
+/**************************************************************************************************
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){ 
@@ -257,7 +259,7 @@ static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){
 } 
 #endif
 
-
+*/
 
 
 #endif