X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.h;fp=indicatorcommand.h;h=0d924fd1ff0a1a17cfa51b6faa5de55dcd3bf186;hb=8173238f9f94af9baab8471de58bed7c8830948d;hp=0000000000000000000000000000000000000000;hpb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
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+#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
+