X-Git-Url: http://source.jalview.org/gitweb/?p=jpred.git;a=blobdiff_plain;f=sources%2Fpairwise%2FPairwise%2FPairwise.xs;fp=sources%2Fpairwise%2FPairwise%2FPairwise.xs;h=e6434645cd1ec65976ce448067ec7178b47a7067;hp=0000000000000000000000000000000000000000;hb=9aa768067094f24f46f273077f867348e6143711;hpb=eb3001dc41bf6cd46e20fd13fe3efbe9dedf6013

diff --git a/sources/pairwise/Pairwise/Pairwise.xs b/sources/pairwise/Pairwise/Pairwise.xs
new file mode 100644
index 0000000..e643464
--- /dev/null
+++ b/sources/pairwise/Pairwise/Pairwise.xs
@@ -0,0 +1,43 @@
+#include "EXTERN.h"
+#include "perl.h"
+#include "XSUB.h"
+
+#include "ppport.h"
+
+#include "../pairwise.h"
+
+#include <strings.h>
+
+MODULE = Pairwise		PACKAGE = Pairwise		
+
+void
+pairwise (file)
+		FILE *file
+	PREINIT:
+		struct fasta **seqs;
+		char **output;
+		int i = 0;
+	PPCODE:
+		/* read the sequences */
+		seqs = read_fasta(file);
+		check_length(seqs);
+
+		/* do the pairwise comparison */
+		output = do_pairwise(seqs);
+
+		/* free the sequences */
+		while (seqs[i] != NULL)
+			free_fasta(seqs[i++]);
+		free(seqs);
+
+		/* find out much output there is */
+		while (output[i] != NULL)
+			i++;
+		EXTEND(SP, i);
+
+		/* convert it to perl and free the output */
+		for (i = 0; output[i] != NULL; i++) {
+			PUSHs(sv_2mortal( newSVpv(output[i], strlen(output[i])) ));
+			free(output[i]);
+		}
+		free(output);