class TreeMap;
class SAbundVector;
class RAbundVector;
+class SequenceDB;
class GlobalData {
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
string getGroupFile();
string getOrderFile();
string getFastaFile();
+ string getNexusFile();
+ string getClustalFile();
string getTreeFile();
string getSharedFile();
string getCutOff();
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();
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, scale;
+
+ 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