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/// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_FORMAT_PARAMFILE_H
#define BALL_FORMAT_PARAMFILE_H
#ifndef BALL_SYSTEM_FILE_H
# include <BALL/SYSTEM/file.h>
#endif
#ifndef BALL_DATATYPE_STRING_H
# include <BALL/DATATYPE/string.h>
#endif
#include <QtXml/QXmlStreamReader>
#include <QtXml/QXmlStreamWriter>
#include <QtCore/QFile>
#include <map>
#include <list>
namespace BALL
{
enum BALL_EXPORT ParameterType
{
INFILE,
OUTFILE,
STRING,
INT,
DOUBLE,
INFILELIST,
OUTFILELIST,
STRINGLIST,
INTLIST,
DOUBLELIST,
GALAXY_OPT_OUTDIR,
GALAXY_OPT_OUTID
};
struct BALL_EXPORT ParameterDescription
{
// constructor
ParameterDescription()
{
name = "";
description = "";
category = "";
mandatory = false;
advanced = false;
type = INFILE;
output_format_source = "";
allowed_values.clear();
supported_formats.clear();
hidden = false;
};
String name;
String description;
String category;
bool mandatory;
bool advanced;
ParameterType type;
/** In case of ouput-files, this variable allows to specify the name of an input-parameter, whose format should be used as ouput-format. \n
Note, that this variable will be used only for the creation of config-files for workflow-systems (Galaxy, Knime, etc.) and not for the command-line interface, where the user will directly specify output-filenames. */
String output_format_source;
/** If this list is empty, then there are no restrictions on the value of the parameter */
list<String> allowed_values;
/** In case of input-/output-files, this list should contain the supported file-extensions. \n
If the list is empty, no format restrictions are set. */
list<String> supported_formats;
// if parameters shall be hidden in galaxy
bool hidden;
};
/** Class for storing and retrieving parameters (e.g. tool-parameters) to an xml-based file */
class BALL_EXPORT ParamFile : public File
{
public:
ParamFile(const String& name, File::OpenMode open_mode);
~ParamFile();
/** Write a section to the output file (e.g. parameters for one tool)
@param section_description a *short* description of this section (e.g. the tool), containing only a few words
@param section_helptext a longer help-text/detailed description can be specified here
@param category the category into which the tool falls (e.g. Docking, QSAR, etc.)
@param descriptions description for all parameters to be saved
@param value values of all parameters to be saved */
void writeSection(String section_name, String section_description, String version, const String& section_helptext,
const String& category, const std::list<std::pair<String,ParameterDescription> >& descriptions,
const std::map<String,list<String> >& values);
/** Read a section from input file (e.g. parameters for one tool)
@param descriptions descriptions of parameters will be stored here
@param values values of parameters will be stored here
@param overwrite_existing if set to true, entries already existing in 'descriptions' and 'values' will be overwritten. */
void readSection(String& section_name, String& section_description, String& version, String& section_helptext,
String& category, std::list<std::pair<String, ParameterDescription> >& descriptions,
std::map<String,list<String> >& values,
bool overwrite_existing=false);
void close();
protected:
String filename_;
File::OpenMode open_mode_;
bool mode_read_;
QXmlStreamReader* xmlIn_;
QXmlStreamWriter* xmlOut_;
QFile* file_;
};
}
#endif
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