added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / shhhseqscommand.h

diff --git a/shhhseqscommand.h b/shhhseqscommand.h
index 1b0211afba43e5577abce79f89704114b3705b2f..4da1a840c7d3c591f589ad6ea0103da4d9fbf1ce 100644 (file)
--- 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"; }
        
        
@@ -97,7 +99,7 @@ struct shhhseqsData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){ 
        shhhseqsData* pDataArray;