modified precluster to use less memory.

[mothur.git] / distclearcut.h

diff --git a/distclearcut.h b/distclearcut.h
new file mode 100644 (file)
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+++ b/distclearcut.h
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+/*
+ * 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
+
+#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);
+
+
+#endif /* _INC_DIST_H_ */
+
+
+
+
+
+
+
+
+