--- /dev/null
+/*
+ * fasta.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_FASTA_H_
+#define _INC_NJ_FASTA_H_ 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include "clearcut.h"
+
+#define NJ_INITIAL_BUFFER_SIZE 512
+#define NJ_INITIAL_NSEQS 64
+
+#define NJ_FASTA_MODE_TITLE 100
+#define NJ_FASTA_MODE_SEQUENCE 101
+#define NJ_FASTA_MODE_NEWLINE 102
+#define NJ_FASTA_MODE_UNKNOWN 103
+
+
+typedef struct _STRUCT_NJ_ALIGNMENT {
+
+ long int nseq;
+ long int length;
+
+ char **titles;
+
+ char *data;
+
+} NJ_alignment;
+
+
+NJ_alignment *
+NJ_read_fasta(NJ_ARGS *nj_args);
+
+void
+NJ_print_alignment(NJ_alignment *alignment);
+
+void
+NJ_free_alignment(NJ_alignment *alignment);
+
+int
+NJ_taxaname_unique(NJ_alignment *alignment);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _INC_NJ_FASTA_H_ */
+
+
+
+