added paralellization for windows to dist.seqs and summary.seqs

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index d519e9154fecadd04d3e535c3cfe6916e03cabba..75b9c2ba8ffa727b84dadbc4ebdd25479e11674c 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -15,7 +15,6 @@
 #include "database.hpp"
 #include "alignment.hpp"
 #include "alignmentdb.h"
-#include "mothurfiles.h"
 
 class AlignCommand : public Command {
        
@@ -23,12 +22,16 @@ public:
        AlignCommand(string);   
        AlignCommand();
        ~AlignCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "align.seqs";                  }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       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"; }
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        struct linePair {
@@ -39,7 +42,6 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        bool MPIWroteAccnos;
-       map<string, vector<string> > outputTypes;
        
        AlignmentDB* templateDB;
        Alignment* alignment;
@@ -59,8 +61,7 @@ private:
        vector<string> candidateFileNames;
        vector<string> outputNames;
        
-       bool abort, flip, calledHelp;
-       CurrentFile* currentFiles;
+       bool abort, flip, calledHelp, save;
 
 };