moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / distclearcut.h

diff --git a/distclearcut.h b/distclearcut.h
deleted file mode 100644 (file)
index e4abef2..0000000
--- a/distclearcut.h
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- * dist.h
- *
- * $Id$
- *
- *****************************************************************************
- *
- * Copyright (c) 2004,  Luke Sheneman
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without 
- * modification, are permitted provided that the following conditions 
- * are met:
- * 
- *  + Redistributions of source code must retain the above copyright 
- *    notice, this list of conditions and the following disclaimer. 
- *  + Redistributions in binary form must reproduce the above copyright 
- *    notice, this list of conditions and the following disclaimer in 
- *    the documentation and/or other materials provided with the 
- *    distribution. 
- *  + The names of its contributors may not be used to endorse or promote 
- *    products derived  from this software without specific prior 
- *    written permission. 
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
- * POSSIBILITY OF SUCH DAMAGE.  
- *
- *****************************************************************************
- *
- * Compute a distance matrix given a set of sequences
- *
- *****************************************************************************
- *
- * AUTHOR:
- * 
- *   Luke Sheneman
- *   sheneman@cs.uidaho.edu
- *
- */
-
-
-#ifndef _INC_DIST_H_
-#define _INC_DIST_H_ 1
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include "fasta.h"
-#include "clearcut.h"
-
-
-
-/* 
- * An arbitrarily large distance to represent distances
- * which are too great to accurately correct.
- */
-#define NJ_BIGDIST 10.0  
-
-
-
-/* some function prototypes */
-DMAT *
-NJ_build_distance_matrix(NJ_ARGS *nj_args);
-
-DMAT *
-NJ_compute_dmat(NJ_ARGS *nj_args,
-               NJ_alignment *alignment);
-
-
-float
-NJ_pw_percentid(NJ_alignment *alignment,
-               long int x,
-               long int y);
-
-long int
-NJ_pw_differences(NJ_alignment *alignment,
-                 long int x,
-                 long int y,
-                 long int *residues);
-
-void
-NJ_no_correction(DMAT *dmat,
-                NJ_alignment *alignment);
-
-void
-NJ_DNA_jc_correction(DMAT *dmat,
-                    NJ_alignment *alignment);
-
-void
-NJ_PROTEIN_jc_correction(DMAT *dmat,
-                        NJ_alignment *alignment);
-
-void
-NJ_DNA_k2p_correction(DMAT *dmat,
-                     NJ_alignment *alignment);
-
-void
-NJ_PROTEIN_kimura_correction(DMAT *dmat,
-                            NJ_alignment *alignment);
-
-void
-NJ_DNA_count_tt(NJ_alignment *alignment,
-               long int x,
-               long int y,
-               long int *transitions,
-               long int *transversions,
-               long int *residues);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _INC_DIST_H_ */
-
-
-
-
-
-
-
-
-