Merge remote-tracking branch 'origin/master'

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 2ffe90d6ab061601b8e1f8ecc89ee24170d02c7e..7c6a4b2965783a8145d311cfae05a150d82c2ce7 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -67,6 +67,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "summary.shared";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
        string getDescription()         { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
@@ -84,15 +85,16 @@ private:
        vector<Calculator*> sumCalculators;     
        InputData* input;
        
-       bool abort, allLines, mult, all, createPhylip;
+       bool abort, allLines, mult, all, createPhylip, subsample;
        set<string> labels; //holds labels to be used
-       string label, calc, groups, sharedfile;
+       string label, calc, groups, sharedfile, output;
        vector<string>  Estimators, Groups, outputNames;
        vector<SharedRAbundVector*> lookup;
        string format, outputDir;
-       int numGroups, processors;
+       int numGroups, processors, subsampleSize, iters;
        int process(vector<SharedRAbundVector*>, string, string);
        int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
+    int printSims(ostream&, vector< vector<double> >&);
 
 };
 
@@ -121,7 +123,7 @@ struct summarySharedData {
        }
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){ 
        summarySharedData* pDataArray;