modified trim.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473..89089ad8686a20a5ee855a1405d4800729ee325a 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();
@@ -75,7 +69,7 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getEnds();
+       string getCountEnds();
        string getProcessors();
        string getSize();
        string getCandidateFile();
@@ -86,12 +80,20 @@ public:
        string getMismatch();
        string getGapopen();
        string getGapextend();
+       string getVertical();
        string getTrump();
        string getSoft();
-       string getFilter();
+       string getHard();
        string getScale();
-
-
+       string getStartPos();
+       string getEndPos();
+       string getMaxAmbig();
+       string getMaxHomoPolymer();
+       string getMinLength();
+       string getMaxLength();
+       string getFlip();
+       string getOligosFile();
+       
        void setListFile(string);
        void setGroupFile(string file); 
        void setPhylipFile(string);
@@ -104,7 +106,7 @@ public:
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
-       void setEnds(string);
+       void setCountEnds(string);
        void setProcessors(string);
 
        void clear(); 
@@ -113,7 +115,7 @@ public:
        
        void parseGlobalData(string, string);
        
-       void parseTreeFile();           //parses through tree file to find names of nodes and number of them
+       void parseTreeFile();   //parses through tree file to find names of nodes and number of them
                                                        //this is required in case user has sequences in the names file that are
                                                        //not included in the tree. 
                                                        //only takes names from the first tree in the tree file and assumes that all trees use the same names.
@@ -121,9 +123,7 @@ public:
                
 private:
 
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, candidatefile, search, ksize, align, match, size;
-       string mismatch, gapopen, gapextend;
+       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, oligoFile;
 
 
        static GlobalData* _uniqueInstance;