changed all shared commands so that they read the shared file generated by the read...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 3b688b43457d318c8f73471bb088d7ad5de1affb..3a469f08cc52dc15ca51e13d9edf23f7a380a752 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:
@@ -35,10 +36,12 @@ public:
        vector<Tree*> gTree;
        SharedListVector* gSharedList;
        SAbundVector* sabund;
+       RAbundVector* rabund;
        GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName;
+       SequenceDB* gSequenceDB;
+       string inputFileName, helpRequest, commandName, vertical;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
@@ -54,6 +57,8 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
+       string getNexusFile();
+       string getClustalFile();
        string getTreeFile();
        string getSharedFile();
        string getCutOff();
@@ -70,18 +75,31 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getScaler();
+       string getEnds();
+       string getProcessors();
+
+       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();
@@ -96,8 +114,10 @@ public:
 
                
 private:
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scaler;
+
+       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;
+
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor