Initial commit for this soft

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@175 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoPCR/ecoPCR.h

@@ -0,0 +1,269 @@
+#ifndef ECOPCR_H_
+#define ECOPCR_H_
+
+#include <stdio.h>
+#include <inttypes.h>
+
+#ifndef H_apat
+#include "../libapat/apat.h"
+#endif
+
+/*****************************************************
+ * 
+ *  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;
+
+/*
+ * 
+ * Taxonomy taxon types
+ * 
+ */
+
+
+typedef struct {
+	int32_t  taxid;
+	int32_t  rank;
+	int32_t	 parent;
+	int32_t  namelength;
+	char     name[1];
+	
+} ecotxformat_t;
+
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	struct ecotxnode  *parent;
+	char              *name;
+} ecotx_t;
+
+typedef struct {
+	int32_t count;
+	ecotx_t taxon[1];
+} ecotxidx_t;
+ 
+	
+/*
+ * 
+ * Taxonomy rank types
+ * 
+ */
+	
+typedef struct {
+	int32_t count;
+	char*   label[1];
+} ecorankidx_t;
+
+/*
+ * 
+ * Taxonomy name types
+ * 
+ */
+
+typedef struct {
+ 	int32_t is_scientificname;
+	int32_t  namelength;
+	int32_t  classlength;
+	int32_t  taxid;
+	char     names[1];	
+} econameformat_t;
+ 
+ 
+ typedef struct {
+ 	char 	*name;
+ 	char 	*classname;
+ 	int32_t is_scientificname;
+ 	struct ecotxnode  *taxon;
+} econame_t;
+
+ 
+typedef struct {
+	int32_t count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+ typedef struct {
+	ecorankidx_t *ranks;
+	econameidx_t *names;
+	ecotxidx_t   *taxons;
+} ecotaxonomy_t;
+
+ 
+/*****************************************************
+ * 
+ *  Function declarations
+ * 
+ *****************************************************/
+
+/*
+ * 
+ * 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);
+                   
+                   
+void   *eco_realloc(void *chunk,
+                    int32_t chunksize,
+                    const char *error_message,
+                    const char *filename,
+                    int32_t    line);
+                    
+void    eco_free(void *chunk,
+                 const char *error_message,
+                 const char *filename,
+                 int32_t    line);
+                 
+void    eco_trace_memory_allocation();
+void    eco_untrace_memory_allocation();
+
+#define ECOMALLOC(size,error_message) \
+	    eco_malloc((size),(error_message),__FILE__,__LINE__)
+	   
+#define ECOREALLOC(chunk,size,error_message) \
+        eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
+        
+#define ECOFREE(chunk,error_message) \
+        eco_free((chunk),(error_message),__FILE__,__LINE__)
+        
+        
+
+
+/*
+ * 
+ * Error managment
+ * 
+ */
+ 
+  
+void ecoError(int32_t,const char*,const char *,int);
+
+#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
+
+#define ECO_IO_ERROR       (1)
+#define ECO_MEM_ERROR      (2)
+#define ECO_ASSERT_ERROR   (3)
+#define ECO_NOTFOUND_ERROR (4)
+
+
+/*
+ * 
+ * Low level Disk access functions
+ * 
+ */
+
+FILE *open_ecorecorddb(const char *filename,
+                       int32_t    *sequencecount,
+                       int32_t    abort_on_open_error);
+                       
+void *read_ecorecord(FILE *,int32_t *recordSize);
+
+
+
+/* 
+ *   Read function in internal binary format
+ */
+
+FILE             *open_ecoseqdb(const char *filename,
+                                int32_t    *sequencecount);
+                                                                
+ecoseq_t         *readnext_ecoseq(FILE *);
+
+ecorankidx_t     *read_rankidx(const char *filename);
+
+econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
+
+
+
+	/**
+	 * Read taxonomy data as formated by the ecoPCRFormat.py script.
+	 * 
+	 * This function is normaly uses internaly by the read_taxonomy
+	 * function and should not be called directly.
+	 * 
+	 * @arg filename  path to the *.tdx file of the reformated db
+	 * 
+	 * @return pointer to a taxonomy index structure
+	 */
+ 
+ecotxidx_t       *read_taxonomyidx(const char *filename);
+
+ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
+
+ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);
+
+int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
+
+ecoseq_t *ecoseq_iterator(const char *prefix);
+
+
+
+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_taxon(ecotx_t *taxon);
+int32_t delete_taxonomy(ecotxidx_t *index);
+
+
+int32_t rank_index(const char* label,ecorankidx_t* ranks);
+
+int32_t  delete_apatseq(SeqPtr pseq);
+PatternPtr buildPattern(const char *pat, int32_t error_max);
+PatternPtr complementPattern(PatternPtr pat);
+
+SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
+
+char *ecoComplementPattern(char *nucAcSeq);
+char *ecoComplementSequence(char *nucAcSeq);
+char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
+
+ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+
+int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
+int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
+
+#endif /*ECOPCR_H_*/