modified trim.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index d427aba4436eae1811be227fe0e59b25a4495be4..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;
@@ -41,7 +37,7 @@ public:
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, helpRequest, commandName, vertical;
+       string inputFileName, helpRequest, commandName, vertical, argv;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
@@ -57,8 +53,6 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
-       string getNexusFile();
-       string getClustalFile();
        string getTreeFile();
        string getSharedFile();
        string getCutOff();
@@ -75,10 +69,10 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getEnds();
+       string getCountEnds();
        string getProcessors();
        string getSize();
-       string getTemplateFile();
+       string getCandidateFile();
        string getSearch();
        string getKSize();
        string getAlign();
@@ -86,14 +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);
@@ -106,7 +106,7 @@ public:
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
-       void setEnds(string);
+       void setCountEnds(string);
        void setProcessors(string);
 
        void clear(); 
@@ -115,7 +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.
@@ -123,9 +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, templatefile, 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;