added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 762b0e10a02b0428e6a3e8119c1e0a2ee0887d84..8a04c96a32ed6fa769a4e14474dfb624451751d1 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -73,7 +73,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "dist.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
        string getDescription()         { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
 
@@ -88,7 +90,7 @@ private:
        };
        vector<linePair> lines;
        
-       void printSims(ostream&, vector< vector<float> >&);
+       void printSims(ostream&, vector< vector<double> >&);
        int process(vector<SharedRAbundVector*>);
        
        vector<Calculator*> matrixCalculators;
@@ -96,12 +98,12 @@ private:
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        string exportFileName, output, sharedfile;
-       int numGroups, processors;
+       int numGroups, processors, iters, subsampleSize;
        ofstream out;
 
-       bool abort, allLines;
+       bool abort, allLines, subsample;
        set<string> labels; //holds labels to be used
-       string outputFile, calc, groups, label, outputDir;
+       string outputFile, calc, groups, label, outputDir, mode;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
        int process(vector<SharedRAbundVector*>, string, string);
        int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
@@ -130,7 +132,7 @@ struct distSharedData {
        }
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){ 
        distSharedData* pDataArray;