X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhseqscommand.h;h=ffd72b9ebdc161291f9705333f018cb56c09559c;hp=7174ac70caf3f55e146d1cdf09e2b15e5b0cfaf4;hb=615301e57c25e241356a9c2380648d117709458d;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/shhhseqscommand.h b/shhhseqscommand.h
index 7174ac7..ffd72b9 100644
--- a/shhhseqscommand.h
+++ b/shhhseqscommand.h
@@ -29,8 +29,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "shhh.seqs";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	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"; }
 	
 	
@@ -75,7 +77,7 @@ struct shhhseqsData {
 	MothurOut* m;
 	int start;
 	int end;
-	int sigma, threadID;
+	int sigma, threadID, count;
 	vector<string> groups;
 	vector<string> mapfileNames;
 	
@@ -93,6 +95,7 @@ struct shhhseqsData {
 		sigma = s;
 		threadID = tid;
 		groups = gr;
+        count=0;
 	}
 };
 
@@ -111,6 +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; }