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/ecoseq.c

@@ -0,0 +1,223 @@
+#include "ecoPCR.h"
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <string.h>
+#include <stdio.h>
+
+static FILE *open_seqfile(const char *prefix,int32_t index);
+
+
+ecoseq_t *new_ecoseq()
+{
+	void *tmp;
+	
+	tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
+	
+	return tmp;
+}
+
+int32_t delete_ecoseq(ecoseq_t * seq)
+{
+	
+	if (seq)
+	{
+		if (seq->AC)
+			ECOFREE(seq->AC,"Free sequence AC");
+			
+		if (seq->DE)
+			ECOFREE(seq->DE,"Free sequence DE");
+			
+		if (seq->SQ)
+			ECOFREE(seq->SQ,"Free sequence SQ");
+			
+		ECOFREE(seq,"Free sequence structure");
+		
+		return 0;
+			
+	}
+	
+	return 1;
+}
+
+ecoseq_t *new_ecoseq_with_data( char *AC,
+								char *DE,
+								char *SQ,
+								int32_t   taxid_idx
+								)
+{
+	ecoseq_t *tmp;
+	int32_t lstr;
+	tmp = new_ecoseq();
+	
+	tmp->taxid=taxid_idx;
+	
+	if (AC)
+		{
+			lstr =strlen(AC);
+			tmp->AC=ECOMALLOC((lstr+1) * sizeof(char),
+			                  "Allocate sequence accession");
+			strcpy(tmp->AC,AC);
+		}
+
+	if (DE)
+		{
+			lstr =strlen(DE);
+			tmp->DE=ECOMALLOC((lstr+1) * sizeof(char),
+			                  "Allocate sequence definition");
+			strcpy(tmp->DE,DE);
+		}
+
+	if (SQ)
+		{
+			lstr =strlen(SQ);
+			tmp->SQ=ECOMALLOC((lstr+1) * sizeof(char),
+			                  "Allocate sequence data");
+			strcpy(tmp->SQ,SQ);
+		}
+	return tmp;
+
+}
+
+/**
+ * ?? used ??
+ **/
+FILE *open_ecoseqdb(const char *filename,
+                    int32_t    *sequencecount)
+{
+	return open_ecorecorddb(filename,sequencecount,1);
+}
+
+ecoseq_t *readnext_ecoseq(FILE *f)
+{
+	char     *compressed=NULL;
+
+	ecoseqformat_t *raw;
+	ecoseq_t *seq;
+	int32_t  comp_status;
+	unsigned long int seqlength;
+	int32_t  rs;
+	
+	raw = read_ecorecord(f,&rs);
+	
+	if (!raw)
+		return NULL;
+		
+	if (is_big_endian())
+	{
+		raw->CSQ_length = swap_int32_t(raw->CSQ_length);
+		raw->DE_length  = swap_int32_t(raw->DE_length);
+		raw->SQ_length  = swap_int32_t(raw->SQ_length);
+		raw->taxid      = swap_int32_t(raw->taxid);
+	}
+	
+	seq = new_ecoseq();
+	
+	seq->taxid = raw->taxid;
+	
+    seq->AC    = ECOMALLOC(strlen(raw->AC) +1,
+                           "Allocate Sequence Accesion number");
+    strncpy(seq->AC,raw->AC,strlen(raw->AC));
+
+                           
+    seq->DE    = ECOMALLOC(raw->DE_length+1,
+                           "Allocate Sequence definition");
+    strncpy(seq->DE,raw->data,raw->DE_length);
+    
+	seqlength = seq->SQ_length = raw->SQ_length;
+    
+    compressed = raw->data + raw->DE_length;
+
+    seq->SQ = ECOMALLOC(seqlength+1,
+                        "Allocate sequence buffer");
+                        
+    comp_status = uncompress((unsigned char*)seq->SQ,
+                             &seqlength,
+                             (unsigned char*)compressed,
+                             raw->CSQ_length);
+    
+    if (comp_status != Z_OK)
+    	ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
+    
+	return seq;
+}
+
+/**
+ * Open the sequences database (.sdx file)
+ * @param	prefix	name of the database (radical without extension) 
+ * @param	index 	integer
+ * 
+ * @return	file object 
+ */
+FILE *open_seqfile(const char *prefix,int32_t index)
+{
+	char           filename_buffer[1024];
+	int32_t        filename_length;
+	FILE           *input;
+	int32_t        seqcount;
+
+	filename_length = snprintf(filename_buffer,
+								1023,
+	                           "%s_%03d.sdx",
+	                           prefix,
+	                           index);
+	                           
+			fprintf(stderr,"# Coucou %s\n",filename_buffer);
+	                           
+
+	if (filename_length >= 1024)
+		ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
+
+	filename_buffer[filename_length]=0;
+		
+	input=open_ecorecorddb(filename_buffer,&seqcount,0);
+	
+	if (input)
+		fprintf(stderr,"# Reading file %s containing %d sequences...\n",
+				filename_buffer,
+				seqcount);
+				
+	return input;
+}
+
+ecoseq_t *ecoseq_iterator(const char *prefix)
+{
+	static FILE    *current_seq_file= NULL;
+	static int32_t current_file_idx = 1;
+	static char    current_prefix[1024];
+	ecoseq_t       *seq;
+	
+	if (prefix)
+	{
+		current_file_idx = 1;
+
+		if (current_seq_file)
+			fclose(current_seq_file);
+			
+		strncpy(current_prefix,prefix,1023);
+		current_prefix[1024]=0;
+		
+		current_seq_file = open_seqfile(current_prefix,
+		 							    current_file_idx);
+		
+		if (!current_seq_file)
+			return NULL;
+			
+	}
+	
+	seq = readnext_ecoseq(current_seq_file);
+	
+	if (!seq && feof(current_seq_file))
+	{
+		current_file_idx++;
+		fclose(current_seq_file);
+		current_seq_file = open_seqfile(current_prefix,
+		 							    current_file_idx);
+		 							    
+		
+		if (current_seq_file)
+			seq = readnext_ecoseq(current_seq_file);
+	}
+	
+	return seq;
+}