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//
// mimarksattributescommand.h
// Mothur
//
// Created by Sarah Westcott on 3/17/15.
// Copyright (c) 2015 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__mimarksattributescommand__
#define __Mothur__mimarksattributescommand__
#include "command.hpp"
struct Package {
bool required;
string groupName;
string name;
Package() { required=false; groupName=""; name=""; }
Package(bool r, string g, string n) : required(r), groupName(g), name(n) {}
~Package() = default;
string getPackageString() {
string r = "mandatory";
if (!required) { r = "optional"; }
string packageString = name + '\t' + groupName + '\t' + r;
return packageString;
}
};
struct Value {
bool required;
string format, description;
Value() { format=""; description=""; required=false; }
Value(bool r, string d, string f) : format(f), description(d), required(r) {}
~Value() = default;
};
struct Group {
string packageName;
map<string, Value> values;
Group() { packageName = ""; }
Group(string p) : packageName(p) {}
~Group() = default;
};
struct Attribute {
string name, harmonizedName, description, format;
vector<Package> packages;
string getPackagesString() {
string packagesString = "";
for (int i = 0; i < packages.size(); i++) {
packagesString += packages[i].getPackageString() + "\n";
}
return packagesString;
}
Attribute() { format=""; description=""; harmonizedName=""; name=""; }
Attribute(string hn, string d, string n, string f) : format(f), harmonizedName(hn), name(n), description(d) {}
~Attribute() = default;
};
/**************************************************************************************************/
class MimarksAttributesCommand : public Command {
public:
MimarksAttributesCommand(string);
~MimarksAttributesCommand(){}
vector<string> setParameters();
string getCommandName() { return "mimarks.attributes"; }
string getCommandCategory() { return "Hidden"; }
string getOutputPattern(string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Mimarks.attributes"; }
string getDescription() { return "Reads bioSample Attributes xml and generates source for get.mimarkspackage command."; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
Attribute readAttribute(ifstream& in);
Package parsePackage(string package);
string trimTags(string& value);
bool abort;
string xmlFile, selectedPackage;
vector<string> outputNames;
};
/**************************************************************************************************/
#endif /* defined(__Mothur__mimarksattributescommand__) */
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