a program to print smith-waterman scores against a query sequence

[fastq-tools.git] / src / swsse2 / swwozniak.h

diff --git a/src/swsse2/swwozniak.h b/src/swsse2/swwozniak.h
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+/******************************************************************\r
+  Copyright 2006 by Michael Farrar.  All rights reserved.\r
+  This program may not be sold or incorporated into a commercial product,\r
+  in whole or in part, without written consent of Michael Farrar.  For \r
+  further information regarding permission for use or reproduction, please \r
+  contact: Michael Farrar at farrar.michael@gmail.com.\r
+*******************************************************************/\r
+\r
+/*\r
+  Written by Michael Farrar, 2006.\r
+  Please send bug reports and/or suggestions to farrar.michael@gmail.com.\r
+*/\r
+\r
+#ifndef INCLUDE_SWWOZNIAK_H\r
+#define INCLUDE_SWWOZNIAK_H\r
+\r
+#include "swsse2.h"\r
+#include "fastalib.h"\r
+\r
+#define MATRIX_ROW_SIZE 32\r
+\r
+SW_DATA *\r
+swWozniakInit (unsigned char   *querySeq,\r
+               int              queryLength,\r
+               signed char     *matrix);\r
+\r
+\r
+void \r
+swWozniakScan (unsigned char   *querySeq,\r
+               int              queryLength,\r
+               FASTA_LIB       *dbLib,\r
+               void            *swData,\r
+               SEARCH_OPTIONS  *options,\r
+               SCORE_LIST      *scores);\r
+\r
+void\r
+swWozniakComplete (SW_DATA *pSwData);\r
+\r
+\r
+#endif /* INCLUDE_SWWOZNIAK_H */\r