changes while testing

[mothur.git] / metastatscommand.h

diff --git a/metastatscommand.h b/metastatscommand.h
index b4800b71d75bcda1bfa5a39db6f8191849d0b348..82a2cd463fab9762b38bb26dabdef11a7e7a4a0a 100644 (file)
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "metastats";                           }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
        string getDescription()         { return "detects differentially abundant features in clinical metagenomic samples"; }
 
@@ -54,6 +56,9 @@ private:
        
        int process(vector<SharedRAbundVector*>&);
        int driver(int, int, vector<SharedRAbundVector*>&);
+    int convertToShared(string filename);
+    int convertToInput(vector<SharedRAbundVector*>&, string);
+    bool convertSharedToInput;
 };
 
 /**************************************************************************************************/
@@ -66,7 +71,7 @@ struct metastatsData {
     vector<string> designMapGroups;
     vector<string> outputNames;
        int start;
-       int num, iters;
+       int num, iters, count;
        float threshold;
        MothurOut* m;
        string sharedfile;
@@ -84,6 +89,7 @@ struct metastatsData {
         designMapGroups = dg;
         iters = i;
         threshold = thr;
+        count=0;
        }
 };
 /**************************************************************************************************/
@@ -97,7 +103,7 @@ static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
                
         //for each combo
                for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
-                       
+                       pDataArray->count++;
                        //get set names
                        string setA = pDataArray->namesOfGroupCombos[c][0]; 
                        string setB = pDataArray->namesOfGroupCombos[c][1];