EMBOSS: added interface

pjotrp · Nov 30, 2009 · e43d66b · e43d66b
1 parent f5f69d3
commit e43d66b
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Showing 2 changed files with 20 additions and 8 deletions.
diff --git a/src/clibs/emboss/src/biolib_getorf.c b/src/clibs/emboss/src/biolib_getorf.c
@@ -34,8 +34,10 @@ static void getorf_AppORF(ajint find, AjPStr *str,
 			  const char *chrseq, ajint pos,
 			  char aa);
 
-
-
+static void getorf_FindORFs(const AjPSeq seq, ajint len, const AjPTrn trnTable,
+			    ajuint minsize, ajuint maxsize, AjPSeqout seqout, 
+			    AjBool sense, AjBool circular, ajint find, 
+			    ajint *orf_no, AjBool methionine, ajint around);
 
 /* types of control codon */
 #define START 1
@@ -50,14 +52,20 @@ static void getorf_AppORF(ajint find, AjPStr *str,
 #define AROUND_INIT_STOP 5
 #define AROUND_END_STOP  6
 
+/* @func biolib_getorf ********************************************************
+******************************************************************************/
+
+ORF *biolib_getorf(AjPSeq seq, AjPTrn table, unsigned int minsize)
+{
+}
 
-/* @prog getorf ***************************************************************
+/* @func getorf_acd ***********************************************************
 **
 ** Finds and extracts open reading frames (ORFs)
 **
 ******************************************************************************/
 
-int getorf_main(int argc, char **argv)
+int getorf_acd(int argc, char **argv)
 {
 
     AjPSeqall seqall;

diff --git a/src/clibs/emboss/src/biolib_getorf.h b/src/clibs/emboss/src/biolib_getorf.h
@@ -6,11 +6,15 @@
   extern "C" {
 #endif
 
-void getorf_FindORFs(const AjPSeq seq, ajint len, const AjPTrn trnTable,
-			    ajuint minsize, ajuint maxsize, AjPSeqout seqout, 
-			    AjBool sense, AjBool circular, ajint find, 
-			    ajint *orf_no, AjBool methionine, ajint around);
+struct ORFstruct {
+  AjPSeq seq;
+  int frame;
+  unsigned int start, stop;
+};
 
+typedef struct ORFstruct ORF;
+
+ORF *biolib_getorf(AjPSeq seq, AjPTrn table, unsigned int minsize);
 
 #ifdef __cplusplus
   }