First commit

pkg/obiapat/obiapat.h

@@ -0,0 +1,134 @@
+#ifndef __obiapat_h__
+#define __obiapat_h__
+
+#include <stdio.h>
+#include <stdint.h>
+
+#include "apat.h"
+
+/*****************************************************
+ * 
+ *  Data type declarations
+ * 
+ *****************************************************/
+
+/*
+ * 
+ *  Sequence types
+ * 
+ */
+
+typedef struct {
+	
+	int32_t  taxid;
+	char     AC[20];
+	int32_t  DE_length;
+	int32_t  SQ_length;
+	int32_t  CSQ_length;
+	
+	char     data[1];
+	
+} ecoseqformat_t;
+
+typedef struct {
+	int32_t taxid;
+	int32_t SQ_length;
+	char    *AC;
+	char    *DE;
+	char    *SQ;
+} ecoseq_t;
+
+
+
+/*****************************************************
+ * 
+ *  Function declarations
+ * 
+ *****************************************************/
+
+void* ecoError(int error,
+               const char* message,
+               const char * filename,
+               int linenumber,
+			   int *errno,
+			   char **error_msg);
+
+#define ECOERROR(code,message,errno,errmsg) \
+    { return ecoError((code),(message),__FILE__,__LINE__,errno,errmsg); }
+
+#define ECO_IO_ERROR       (1)
+#define ECO_MEM_ERROR      (2)
+#define ECO_ASSERT_ERROR   (3)
+#define ECO_NOTFOUND_ERROR (4)
+
+
+/*
+ * 
+ * Low level system functions
+ * 
+ */
+
+int32_t is_big_endian();
+int32_t swap_int32_t(int32_t);
+
+void   *eco_malloc(int32_t chunksize,
+                   const char *error_message,
+                   const char *filename,
+                   int32_t    line, 
+				   int *errno, char **errmsg);
+                   
+                   
+void   *eco_realloc(void *chunk,
+                    int32_t chunksize,
+                    const char *error_message,
+                    const char *filename,
+                    int32_t    line, 
+				   int *errno, char **errmsg);
+                    
+void    eco_free(void *chunk,
+                 const char *error_message,
+                 const char *filename,
+                 int32_t    line, 
+				 int *errno, char **errmsg);
+                 
+void    eco_trace_memory_allocation();
+void    eco_untrace_memory_allocation();
+
+#define ECOMALLOC(size,error_message,errno,errmsg) \
+	    eco_malloc((size),(error_message),__FILE__,__LINE__,errno,errmsg)
+	   
+#define ECOREALLOC(chunk,size,error_message,errno,errmsg) \
+        eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__,errno,errmsg)
+        
+#define ECOFREE(chunk,error_message,errno,errmsg) \
+        eco_free((chunk),(error_message),__FILE__,__LINE__,errno,errmsg)
+        
+
+
+
+ecoseq_t *new_ecoseq();
+int32_t   delete_ecoseq(ecoseq_t *);
+ecoseq_t *new_ecoseq_with_data( char *AC,
+								char *DE,
+								char *SQ,
+								int32_t   taxid
+								);
+
+
+
+int32_t  delete_apatseq(SeqPtr pseq, 
+				   int *errno, char **errmsg);
+PatternPtr buildPattern(const char *pat, int32_t error_max, int *errno, char **errmsg);
+PatternPtr complementPattern(PatternPtr pat, int *errno, char **errmsg);
+
+SeqPtr new_apatseq(const char *in,int32_t circular, int32_t seqlen,
+                    SeqPtr out, 
+					int *errno, char **errmsg);
+					
+char *ecoComplementPattern(char *nucAcSeq);
+char *ecoComplementSequence(char *nucAcSeq);
+char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end, 
+				   int *errno, char **errmsg);
+
+
+#endif /* __obiapat_h__ */