PDS: update citation fields

[mothur.git] / chimeraperseuscommand.h

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 84563ac6ecc006ca7150f7f5e025b340da964fdf..b6957e39d45cc877a9bee28cccf933af6d86f49e 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -28,8 +28,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.perseus";             }
        string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Chimera.perseus\n"; }
+       string getCitation() { return "Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.perseus\n"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
@@ -44,7 +45,7 @@ private:
        
        bool abort;
        string fastafile, groupfile, outputDir, namefile;
-       int processors;
+       int processors, alignLength;
        double cutoff, alpha, beta;
        
        vector<string> outputNames;
@@ -98,7 +99,7 @@ struct perseusData {
        }
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){ 
        perseusData* pDataArray;