changed added group output to indicator command. a few changes to work with the guy

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b455761ed6fdcf2e8c11a6bcbb52b1704caee464..5432d00564b2151fabaf09e9d16258dff0d298ae 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -1,6 +1,5 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-
 /*
  *  aligncommand.h
  *  Mothur
@@ -10,7 +9,6 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "database.hpp"
 #include "alignment.hpp"
@@ -36,6 +34,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "align.seqs";                  }
        string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
        string getDescription()         { return "align sequences"; }
@@ -57,7 +56,6 @@ private:
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
-       void appendAlignFiles(string, string); 
        void appendReportFiles(string, string);
        
        #ifdef USE_MPI
@@ -120,7 +118,7 @@ struct alignData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){ 
        alignData* pDataArray;