Manage sequence circularity

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@166 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoPCR/ecoPCR.h

@@ -251,7 +251,7 @@ 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);
+SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
 
 char *ecoComplementPattern(char *nucAcSeq);
 char *ecoComplementSequence(char *nucAcSeq);

src/libecoPCR/ecoapat.c

@@ -54,6 +54,9 @@ void EncodeSequence(SeqPtr seq)
 
             cseq++;
         }
+        
+        for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++)
+            *data++ = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
 
         for (i = 0 ; i < MAX_PATTERN ; i++)
             seq->hitpos[i]->top = seq->hiterr[i]->top = 0;
@@ -63,7 +66,7 @@ void EncodeSequence(SeqPtr seq)
 #undef IS_UPPER
 
 
-SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out)
+SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular)
 {
         int    i;
 
@@ -83,20 +86,22 @@ SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out)
 	        }
 		}
 
+		
 		out->name    = in->AC;
 		out->seqsiz = out->seqlen = in->SQ_length;
-
+		out->circular = circular;
+		
 		if (!out->data)
 		{
-			out->data = ECOMALLOC(out->seqlen *sizeof(UInt8),
+			out->data = ECOMALLOC((out->seqlen+circular) *sizeof(UInt8),
 		    	     			  "Error in Allocation of a new Seq data member");    
-		   	out->datsiz=  out->seqlen;
+		   	out->datsiz=  out->seqlen+circular;
 		}
-		else if (out->seqlen >= out->datsiz)
+		else if ((out->seqlen +circular) >= out->datsiz)
 		{
-			out->data = ECOREALLOC(out->data,out->seqlen,
+			out->data = ECOREALLOC(out->data,(out->seqlen+circular),
 			                      "Error during Seq data buffer realloc");
-		   	out->datsiz=  out->seqlen;			                      
+		   	out->datsiz=  out->seqlen+circular;			                      
 		}
 
 		out->cseq = in->SQ;
@@ -191,4 +196,4 @@ PatternPtr complementPattern(PatternPtr pat)
 	
 	return pattern;
 		
-}
+}

src/libecoPCR/ecodna.c

@@ -109,22 +109,44 @@ char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
 	static int32_t buffSize= 0;
 	int32_t length;
 	
-	length = end - begin;
-	
-	if (length >= buffSize)
+	if (begin < end)
 	{
-		buffSize = length+1;
-		if (buffer)
-			buffer=ECOREALLOC(buffer,buffSize,
-					   	      "Error in reallocating sub sequence buffer");
-		else
-			buffer=ECOMALLOC(buffSize,
-			          		 "Error in allocating sub sequence buffer");
-			
+		length = end - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		
+		strncpy(buffer,nucAcSeq + begin,length);
+		buffer[length]=0;
+	}
+	else
+	{
+		length = end + strlen(nucAcSeq) - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		strncpy(buffer,nucAcSeq+begin,length - end);
+		strncpy(buffer+(length-end),nucAcSeq ,end);
+		buffer[length]=0;
 	}
-	
-	strncpy(buffer,nucAcSeq + begin,length);
-	buffer[length]=0;
 	
 	return buffer;
 }