From 8455ed0a99653ff4970a7623d8b0ac97e26178f1 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 14 Jun 2007 14:11:13 +0000
Subject: [PATCH] git-svn-id:
 https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@66
 60f365c0-8329-0410-b2a4-ec073aeeaa1d

---
 src/ecogrep.c | 43 ++++++++++++++++++++-----------------------
 1 file changed, 20 insertions(+), 23 deletions(-)

diff --git a/src/ecogrep.c b/src/ecogrep.c
index 5752568..15bbbf6 100644
--- a/src/ecogrep.c
+++ b/src/ecogrep.c
@@ -145,10 +145,10 @@ int main(int argc, char **argv){
 	char			*stream				= ECOMALLOC(sizeof(char *)*LINE_BUFF_SIZE,"error stream buffer allocation"); 
 	char			*orig				= ECOMALLOC(sizeof(char *)*LINE_BUFF_SIZE,"error orig buffer allocation"); 
 
-	int 			is_ignored 		= 0;		
+	int 			is_ignored 			= 0;		
 	int				is_included			= 0;
 	int				is_matching			= 0;
-		
+	int				good				= 0;
 	seq = new_ecoseq();
 	
 	/**
@@ -275,42 +275,39 @@ int main(int argc, char **argv){
 				getLineContent(stream,seq);	
 				
 				/* -----------------------------------------------*/
-				/* ignored if :									  */
-				/*  - v mode and no ignored						  */
-				/*	OR											  */
-				/* 	- at least one -i option used				  */
+				/* is ignored if at least one option -i 		  */
 				/*  AND											  */
-				/*  - -i option is parent of current taxid		  */
+				/* if current sequence is son of taxid 		 	  */
 				/* -----------------------------------------------*/ 	
-			    is_ignored = ( (v && i==0) || 
-			    			   ( (i > 0) && (eco_is_taxid_included(	taxonomy, 
+			    is_ignored = ( (i > 0) && (eco_is_taxid_included(	taxonomy, 
 			                            							ignored_taxid, 
 			                            							i, 
 			                            							seq->taxid))
-			                   )
 			                 );				
 
 				/* -----------------------------------------------*/
-				/* included if :								  */
-				/* 	- normal mode and no restriction			  */
+				/* is included if no -r option					  */
 				/*  OR											  */
-				/*  - is -r option	is parent of current taxid	  */
+				/*  if current sequence is son of taxid			  */
 				/* -----------------------------------------------*/ 				
-				is_included = ( (!v && (r == 0)) || (eco_is_taxid_included(	taxonomy, 
+				is_included = ( (r == 0) || (eco_is_taxid_included(	taxonomy, 
 			                            									restricted_taxid, 
 			                            	 								r, 
 			                            									seq->taxid))
 			                  );
 
-				/* -----------------------------------------------*/
-				/* match if no pattern or if function return 1    */
-				/* -----------------------------------------------*/ 
-			    is_matching = ( (!v && !p) || (ispatternmatching(seq,pattern)));
-			        								
-				if 	( 
-						(!v && (!is_ignored && is_included && is_matching) ) ||
-						( v && (is_ignored && !is_included && !is_matching) )
-				  	)
+				/* ----------------------------------------------------------- */
+				/* match if no pattern or if pattern match current sequence    */
+				/* ----------------------------------------------------------- */ 
+			    is_matching = ( !p || (ispatternmatching(seq,pattern)));
+			        			
+			        			
+			    good = (is_included  && 	is_matching && 	!is_ignored);
+			    
+			    if (v)
+			       good=!good;
+			       			
+				if 	( good )
 				{
 					printf("%s",orig);
 	     			matchingresult++;