Revision 65e147fc67310f2f53bbe1c8fc89ab94b02570dc authored by Ronny Lorenz on 04 May 2015, 13:34:04 UTC, committed by Ronny Lorenz on 04 May 2015, 13:34:04 UTC
1 parent 48c40ba
convert_epars.h
#ifndef __VIENNA_RNA_PACKAGE_CONVERT_EPARS_H__
#define __VIENNA_RNA_PACKAGE_CONVERT_EPARS_H__
/**
* \file convert_epars.h
* \brief Functions and definitions for energy parameter file format conversion
*/
/** Flag to indicate printing of a complete parameter set */
#define VRNA_CONVERT_OUTPUT_ALL 1U
/** Flag to indicate printing of hairpin contributions */
#define VRNA_CONVERT_OUTPUT_HP 2U
/** Flag to indicate printing of base pair stack contributions */
#define VRNA_CONVERT_OUTPUT_STACK 4U
/** Flag to indicate printing of hairpin mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_HP 8U
/** Flag to indicate printing of interior loop mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_INT 16U
/** Flag to indicate printing of 1:n interior loop mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_INT_1N 32U
/** Flag to indicate printing of 2:3 interior loop mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_INT_23 64U
/** Flag to indicate printing of multi loop mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_MULTI 128U
/** Flag to indicate printing of exterior loop mismatch contribution */
#define VRNA_CONVERT_OUTPUT_MM_EXT 256U
/** Flag to indicate printing of 5' dangle conctribution */
#define VRNA_CONVERT_OUTPUT_DANGLE5 512U
/** Flag to indicate printing of 3' dangle contribution */
#define VRNA_CONVERT_OUTPUT_DANGLE3 1024U
/** Flag to indicate printing of 1:1 interior loop contribution */
#define VRNA_CONVERT_OUTPUT_INT_11 2048U
/** Flag to indicate printing of 2:1 interior loop contribution */
#define VRNA_CONVERT_OUTPUT_INT_21 4096U
/** Flag to indicate printing of 2:2 interior loop contribution */
#define VRNA_CONVERT_OUTPUT_INT_22 8192U
/** Flag to indicate printing of bulge loop contribution */
#define VRNA_CONVERT_OUTPUT_BULGE 16384U
/** Flag to indicate printing of interior loop contribution */
#define VRNA_CONVERT_OUTPUT_INT 32768U
/** Flag to indicate printing of multi loop contribution */
#define VRNA_CONVERT_OUTPUT_ML 65536U
/** Flag to indicate printing of misc contributions (such as terminalAU) */
#define VRNA_CONVERT_OUTPUT_MISC 131072U
/** Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops) */
#define VRNA_CONVERT_OUTPUT_SPECIAL_HP 262144U
/** Flag to indicate printing of given parameters only\n\note This option overrides all other output options, except #VRNA_CONVERT_OUTPUT_DUMP ! */
#define VRNA_CONVERT_OUTPUT_VANILLA 524288U
/** Flag to indicate printing of interior loop asymmetry contribution */
#define VRNA_CONVERT_OUTPUT_NINIO 1048576U
/** Flag to indicate dumping the energy contributions from the library instead of an input file */
#define VRNA_CONVERT_OUTPUT_DUMP 2097152U
/**
* Convert/dump a Vienna 1.8.4 formatted energy parameter file
*
* The options argument allows to control the different output modes.\n
* Currently available options are:\n
* #VRNA_CONVERT_OUTPUT_ALL, #VRNA_CONVERT_OUTPUT_HP, #VRNA_CONVERT_OUTPUT_STACK\n
* #VRNA_CONVERT_OUTPUT_MM_HP, #VRNA_CONVERT_OUTPUT_MM_INT, #VRNA_CONVERT_OUTPUT_MM_INT_1N\n
* #VRNA_CONVERT_OUTPUT_MM_INT_23, #VRNA_CONVERT_OUTPUT_MM_MULTI, #VRNA_CONVERT_OUTPUT_MM_EXT\n
* #VRNA_CONVERT_OUTPUT_DANGLE5, #VRNA_CONVERT_OUTPUT_DANGLE3, #VRNA_CONVERT_OUTPUT_INT_11\n
* #VRNA_CONVERT_OUTPUT_INT_21, #VRNA_CONVERT_OUTPUT_INT_22, #VRNA_CONVERT_OUTPUT_BULGE\n
* #VRNA_CONVERT_OUTPUT_INT, #VRNA_CONVERT_OUTPUT_ML, #VRNA_CONVERT_OUTPUT_MISC\n
* #VRNA_CONVERT_OUTPUT_SPECIAL_HP, #VRNA_CONVERT_OUTPUT_VANILLA, #VRNA_CONVERT_OUTPUT_NINIO\n
* #VRNA_CONVERT_OUTPUT_DUMP
*
* The defined options are fine for bitwise compare- and assignment-operations,
* e. g.: pass a collection of options as a single value like this:
* \verbatim convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) \endverbatim
*
* \param iname The input file name (If NULL input is read from stdin)
* \param oname The output file name (If NULL output is written to stdout)
* \param options The options (as described above)
*/
void convert_parameter_file(const char *iname,
const char *oname,
unsigned int options);
#endif
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