#ifndef GLOBALDATA_HPP
#define GLOBALDATA_HPP
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#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;
+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();
string getGroupFile();
string getOrderFile();
string getFastaFile();
+ string getNexusFile();
+ string getClustalFile();
string getTreeFile();
string getSharedFile();
string getCutOff();
string getFreq();
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&);