added screen.seqs command - pds

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 3b688b43457d318c8f73471bb088d7ad5de1affb..f97d98b311ff46f21d5479c15795eaa3e69fd892 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, argv;
        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 +75,43 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getScaler();
+       string getCountEnds();
+       string getProcessors();
+       string getSize();
+       string getCandidateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
+       string getVertical();
+       string getTrump();
+       string getSoft();
+       string getHard();
+       string getScale();
+       string getStartPos();
+       string getEndPos();
+       string getMaxAmbig();
+       string getMaxHomoPolymer();
+       string getMinLength();
+       string getMaxLength();
 
        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 setCountEnds(string);
+       void setProcessors(string);
 
        void clear(); 
        void clearLabels();
@@ -89,15 +119,16 @@ 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.
 
                
 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, 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;
+
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor