--- /dev/null
+/*
+ * njdist.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.
+ *
+ *****************************************************************************
+ *
+ * AUTHOR:
+ *
+ * Luke Sheneman
+ * sheneman@cs.uidaho.edu
+ *
+ */
+
+
+#ifndef _INC_NJ_CMDARGS_H_
+#define _INC_NJ_CMDARGS_H_ 1
+
+#include "clearcut.h"
+
+
+/* some datatypes */
+typedef struct _STRUCT_NJ_ARGS {
+
+ char *infilename; /* the name of the input file */
+ char *outfilename; /* the name of the output tree */
+ char *matrixout; /* the name of the distance matrix output file */
+
+ int input_mode;
+ int aligned_flag;
+
+ int verbose_flag;
+ int quiet_flag;
+
+ int stdin_flag;
+ int stdout_flag;
+
+ int help;
+ int version;
+
+ int norandom;
+ int shuffle;
+
+ int dna_flag;
+ int protein_flag;
+
+ int seed;
+
+ /* correction models for distance */
+ int correction_model;
+ int jukes_flag;
+ int kimura_flag;
+
+ /* flag for using traditional neighbor-joining */
+ int neighbor;
+
+ /* number of trees to output */
+ int ntrees;
+
+ /* exponential notation output */
+ int expblen; /* exp notation for tree branch lengths */
+ int expdist; /* exp notation for distances in matrix output */
+
+} NJ_ARGS;
+
+
+
+/* some function prototypes */
+
+NJ_ARGS *
+NJ_handle_args(int argc,
+ char *argv[]);
+
+void
+NJ_print_args(NJ_ARGS *nj_args);
+
+void
+NJ_usage(void);
+
+
+#endif /* _INC_NJ_CMDARGS_H_ */
+