modified precluster to use less memory.

[mothur.git] / fasta.h

diff --git a/fasta.h b/fasta.h
new file mode 100644 (file)
index 0000000..29ea288
--- /dev/null
+++ b/fasta.h
@@ -0,0 +1,89 @@
+/*
+ * 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
+
+#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);
+
+#endif /* _INC_NJ_FASTA_H_ */
+
+
+
+