vector<string> setParameters();
string getCommandName() { return "dist.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
string getDescription() { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
};
vector<linePair> lines;
- void printSims(ostream&, vector< vector<float> >&);
+ void printSims(ostream&, vector< vector<double> >&);
int process(vector<SharedRAbundVector*>);
vector<Calculator*> matrixCalculators;
InputData* input;
vector<SharedRAbundVector*> lookup;
string exportFileName, output, sharedfile;
- int numGroups, processors;
+ int numGroups, processors, iters, subsampleSize;
ofstream out;
- bool abort, allLines;
+ bool abort, allLines, subsample;
set<string> labels; //holds labels to be used
- string outputFile, calc, groups, label, outputDir;
+ string outputFile, calc, groups, label, outputDir, mode;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used
int process(vector<SharedRAbundVector*>, string, string);
int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
/**************************************************************************************************/
//custom data structure for threads to use.
-//main process handling the calcs that can do more than 2 groups
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct distSharedData {
}
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){
distSharedData* pDataArray;