changed defaults in allign.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 40b87583aaa2e472f788b2102f5daea0628c2f9e..b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -23,6 +23,7 @@ class GroupMap;
 class TreeMap;
 class SAbundVector;
 class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -39,7 +40,8 @@ public:
        GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName, vertical;
+       SequenceDB* gSequenceDB;
+       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
@@ -73,25 +75,37 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-
+       string getEnds();
+       string getProcessors();
+       string getSize();
+       string getCandidateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
        string getTrump();
        string getSoft();
        string getFilter();
-       
-
        string getScale();
 
 
        void setListFile(string);
+       void setGroupFile(string file); 
        void setPhylipFile(string);
        void setColumnFile(string);
        void setNameFile(string);
        void setRabundFile(string);
        void setSabundFile(string);
+       void setSharedFile(string);
        void setFormat(string);
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
+       void setEnds(string);
+       void setProcessors(string);
 
        void clear(); 
        void clearLabels();
@@ -108,7 +122,8 @@ 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;
+       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;
 
 
        static GlobalData* _uniqueInstance;