changing command name classify.shared to classifyrf.shared

[mothur.git] / shhhseqscommand.h

diff --git a/shhhseqscommand.h b/shhhseqscommand.h
index a4695be5934eddf0fab5da392fe587b1a8199432..ffd72b9ebdc161291f9705333f018cb56c09559c 100644 (file)
--- a/shhhseqscommand.h
+++ b/shhhseqscommand.h
@@ -29,9 +29,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "shhh.seqs";   }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Shhh.seqs"; }
+    string getOutputPattern(string);   
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
        string getDescription()         { return "shhh.seqs"; }
        
        
@@ -76,7 +77,7 @@ struct shhhseqsData {
        MothurOut* m;
        int start;
        int end;
-       int sigma, threadID;
+       int sigma, threadID, count;
        vector<string> groups;
        vector<string> mapfileNames;
        
@@ -94,6 +95,7 @@ struct shhhseqsData {
                sigma = s;
                threadID = tid;
                groups = gr;
+        count=0;
        }
 };
 
@@ -112,6 +114,8 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
                //precluster each group
                for (int k = pDataArray->start; k < pDataArray->end; k++) {
                        
+            pDataArray->count++;
+            
                        int start = time(NULL);
                        
                        if (pDataArray->m->control_pressed) {  return 0; }