JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / pairwise / Pairwise / Pairwise.xs

diff --git a/sources/pairwise/Pairwise/Pairwise.xs b/sources/pairwise/Pairwise/Pairwise.xs
new file mode 100644 (file)
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);