added trim.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index f97d98b311ff46f21d5479c15795eaa3e69fd892..2a57310ccc301f490f007680a93e64ee1b0157cf 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,14 +4,10 @@
 #include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
-
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 
-
-using namespace std;
-
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
@@ -57,8 +53,6 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
-       string getNexusFile();
-       string getClustalFile();
        string getTreeFile();
        string getSharedFile();
        string getCutOff();
@@ -97,7 +91,12 @@ public:
        string getMaxHomoPolymer();
        string getMinLength();
        string getMaxLength();
-
+       string getFlip();
+       string getForwardMismatch();
+       string getReverseMismatch();
+       string getBarcodeMismatch();
+       string getOligosFile();
+       
        void setListFile(string);
        void setGroupFile(string file); 
        void setPhylipFile(string);
@@ -127,7 +126,7 @@ public:
                
 private:
 
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer, flip, forMismatch, revMismatch, barMismatch, oligoFile;
 
 
        static GlobalData* _uniqueInstance;