modified precluster to use less memory.

[mothur.git] / cmdargs.h

diff --git a/cmdargs.h b/cmdargs.h
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+/*
+ * 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_ */
+