X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473;hb=6f9dc7ca71d7b8ed4aba2824f76ae6b29da89f3b;hp=309ab4a09c712132617c1fab8bd96e7849f4643b;hpb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 309ab4a..b3b0798 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -5,36 +5,48 @@
 #include "groupmap.h"
 #include "treemap.h"
 
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+
+
 using namespace std;
 
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
 class Tree;
 class OrderVector;
 class InputData;
 class GroupMap;
 class TreeMap;
 class SAbundVector;
+class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
 	static GlobalData* getInstance();
-	ListVector* getListVector();
-	SparseMatrix* getSparseMatrix();
+	ListVector* gListVector;
+	SparseMatrix* gSparseMatrix;
 	InputData* ginput;
 	OrderVector* gorder;
 	ListVector* glist;
 	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
 	set<string> labels; //holds labels to be used
+	vector<string> Treenames;
 	
 	string getPhylipFile();
 	string getColumnFile();
@@ -45,6 +57,8 @@ public:
 	string getGroupFile();
 	string getOrderFile();
 	string getFastaFile();
+	string getNexusFile();
+	string getClustalFile();
 	string getTreeFile();
 	string getSharedFile();
 	string getCutOff();
@@ -58,39 +72,67 @@ public:
 	string getAbund();
 	string getRandomTree();
 	string getGroups();
+	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 setListVector(ListVector*);
-	void setSparseMatrix(SparseMatrix*);
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
 	
 	void parseGlobalData(string, string);
+	
+	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;
+
+	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;
+
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
 	void operator=( const GlobalData& ); // Disable assignment operator
 	GlobalData();
 	~GlobalData();
-	ListVector* gListVector;
-	SparseMatrix* gSparseMatrix;
 	void reset();	//clears all non filename parameters
+	void readTreeString(ifstream&);