Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / clustal / ktuple_pair.h

diff --git a/binaries/src/clustalo/src/clustal/ktuple_pair.h b/binaries/src/clustalo/src/clustal/ktuple_pair.h
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+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ *  RCS $Id: ktuple_pair.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+/* K-Tuple code for pairwise alignment (Wilbur and Lipman (1983)
+ * Most code taken from showpair (Clustal 1.83)
+ */
+
+
+#ifndef CLUSTALO_KTUPLE_PAIR_H
+#define CLUSTALO_KTUPLE_PAIR_H
+
+#include "seq.h"
+#include "symmatrix.h"
+#include "progress.h"
+
+typedef struct {
+    int ktup;
+    int window;
+    int wind_gap;
+    int signif;
+} ktuple_param_t;
+
+
+extern void
+KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq,
+               int istart, int iend,
+               int jstart, int jend,
+               ktuple_param_t *aln_param,
+               progress_t *prProgress, 
+                          unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
+
+#endif