Initial commit

Makefile.am

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+SUBDIRS=phyml levmar seqgen librna src
+
+docu_DATA = INSTALL README AUTHORS COPYING TODO 
+
+EXTRA_DIST = INSTALL README AUTHORS COPYING TODO 
+
+docudir = $(pkgdatadir)

TODO.org

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+* TODO Re-implement current algorithm in matrix
+* TODO Check score distributions
+* TODO Add penalty for stop codons
+* TODO Add frame-score
+* TODO Set up test-sets
+** TODO Alignments/annotations
+*** TODO Fly
+*** TODO Human
+*** TODO Plasmodium
+** TODO Statistics

autogen.sh

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+# Inits project from configure.ac
+aclocal
+autoheader
+automake -a
+autoconf

configure.ac

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+AC_INIT(RNAcode, 0.1, wash@tbi.univie.ac.at, RNAcode)
+AM_INIT_AUTOMAKE
+
+AC_PROG_CC
+
+
+if test "$GCC" = yes; then
+  AC_DEFINE(UNUSED, __attribute__ ((unused)), avoid warning about unused variables)
+else
+  AC_DEFINE(UNUSED,, only for gcc)
+fi
+
+AC_SUBST(VERSION)
+ISODATE=`date +%Y-%m-%d`
+AC_SUBST(ISODATE)
+
+
+AC_HEADER_STDC
+AC_CHECK_HEADERS(malloc.h strings.h unistd.h)
+AC_C_CONST
+AC_TYPE_SIZE_T
+AC_INLINE
+
+AC_CHECK_FUNCS(strdup strstr strchr erand48)
+
+AC_PROG_CXX
+
+AC_PROG_RANLIB
+
+AC_PROG_INSTALL
+
+AC_CONFIG_HEADERS(config.h) 
+
+AC_OUTPUT([Makefile phyml/Makefile levmar/Makefile seqgen/Makefile src/Makefile librna/Makefile])
+
+

levmar/Axb.c

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+/////////////////////////////////////////////////////////////////////////////////
+// 
+//  Solution of linear systems involved in the Levenberg - Marquardt
+//  minimization algorithm
+//  Copyright (C) 2004  Manolis Lourakis (lourakis@ics.forth.gr)
+//  Institute of Computer Science, Foundation for Research & Technology - Hellas
+//  Heraklion, Crete, Greece.
+//
+//  This program is free software; you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation; either version 2 of the License, or
+//  (at your option) any later version.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+//
+/////////////////////////////////////////////////////////////////////////////////
+
+/******************************************************************************** 
+ * LAPACK-based implementations for various linear system solvers. The same core
+ * code is used with appropriate #defines to derive single and double precision
+ * solver versions, see also Axb_core.c
+ ********************************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+#include "lm.h"
+#include "misc.h"
+
+/* double precision definitions */
+#define LM_REAL double
+#define LM_PREFIX d
+#define CNST(x) (x)
+#ifndef HAVE_LAPACK
+#include <float.h>
+#define LM_REAL_EPSILON DBL_EPSILON
+#endif
+
+#include "Axb_core.c"
+
+#undef LM_REAL
+#undef LM_PREFIX
+#undef CNST
+#undef LM_REAL_EPSILON
+
+/* single precision (float) definitions */
+#define LM_REAL float
+#define LM_PREFIX s
+#define SUBCNST(x) x##F
+#define CNST(x) SUBCNST(x) // force substitution
+#ifndef HAVE_LAPACK
+#define LM_REAL_EPSILON FLT_EPSILON
+#endif
+
+#include "Axb_core.c"
+
+#undef LM_REAL
+#undef LM_PREFIX
+#undef SUBCNST
+#undef CNST
+#undef LM_REAL_EPSILON