added indicator command

[mothur.git] / indicatorcommand.h

diff --git a/indicatorcommand.h b/indicatorcommand.h
new file mode 100644 (file)
index 0000000..0d924fd
--- /dev/null
+++ b/indicatorcommand.h
@@ -0,0 +1,56 @@
+#ifndef INDICATORCOMMAND_H
+#define INDICATORCOMMAND_H
+
+/*
+ *  indicatorcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "readtree.h"
+#include "treemap.h"
+#include "globaldata.hpp"
+#include "sharedrabundvector.h"
+#include "sharedrabundfloatvector.h"
+#include "inputdata.h"
+
+class IndicatorCommand : public Command {
+public:
+       IndicatorCommand(string);
+       IndicatorCommand();
+       ~IndicatorCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       GlobalData* globaldata;
+       ReadTree* read;
+       TreeMap* treeMap;
+       string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
+       bool abort, pickedGroups;
+       vector<string> outputNames, Groups;
+       map<string, vector<string> > outputTypes;
+       vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
+       
+       int getShared();
+       int getSharedFloat();
+       int GetIndicatorSpecies(Tree*&);
+       set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
+       vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
+       vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
+       map<int, float> getLengthToLeaf(Tree*&);
+       
+};
+
+
+#endif
+