sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 8af539ba01ae59ed07027d63f2bd9d1859b4c217..90f120602e70dc04600b3048bab41bde21b21edc 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"; }
 
@@ -101,7 +103,7 @@ private:
 
        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> >&);
@@ -119,6 +121,7 @@ struct distSharedData {
        unsigned long long start;
        unsigned long long end;
        MothurOut* m;
+    int count;
        
        distSharedData(){}
        distSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -127,6 +130,7 @@ struct distSharedData {
                end = en;
         Estimators = est;
         thisLookup = lu;
+        count = 0;
        }
 };
 /**************************************************************************************************/
@@ -228,7 +232,7 @@ static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){
                        
                vector<SharedRAbundVector*> subset;
                for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
-                       
+                       pDataArray->count++;
                        for (int l = 0; l < k; l++) {
                                
                                if (k != l) { //we dont need to similiarity of a groups to itself