WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / convert_epars.h

diff --git a/binaries/src/ViennaRNA/H/convert_epars.h b/binaries/src/ViennaRNA/H/convert_epars.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/H/convert_epars.h
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+#ifndef __VIENNA_RNA_PACKAGE_CONVERT_EPARS_H__
+#define __VIENNA_RNA_PACKAGE_CONVERT_EPARS_H__
+
+/**
+ *  \addtogroup energy_parameters_convert
+ *  \brief  Convert energy parameter files into the latest format
+ *
+ *  To preserve some backward compatibility the RNAlib also provides
+ *  functions to convert energy parameter files from the format used
+ *  in version 1.4-1.8 into the new format used since version 2.0
+ *
+ *  @{
+ *  \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