[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Mar 12 14:51:35 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv5161/src/main/ca/ucalgary/services/util

Modified Files:
	ACDFile.java 
Log Message:
Added fix to parse variable blocks in ACD files (e.g. emma)
moby-live/Java/src/main/ca/ucalgary/services/util ACDFile.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/ACDFile.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/ACDFile.java	2007/03/10 00:33:16	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/ACDFile.java	2007/03/12 18:51:35	1.4
@@ -206,7 +206,7 @@
 		for(line = reader.readLine(); line != null; line = reader.readLine()){
 		    if(line.matches("^\\s*]")){
 			if(subsection){
-			    System.err.println("Ignoring subsection:\n" + blockText.toString());
+			    //System.err.println("Ignoring subsection:\n" + blockText.toString());
 			    break; // ignore subsection specifications (MOBY 2ndary params don't hav'em)
 			}
 			Map<String,String> block = acdBlockToTagValuePairs(blockText.toString());
@@ -218,6 +218,11 @@
 		    blockText.append(line+"\n");
 		}		
 	    }
+	    else if(line.matches("^\\s*variable:\\s*\\S+\\s+\".*\"\\s*$")){
+		// Ignore variable declarations (for the moment)
+		// since EMBOSS will figure out their values for itself,
+		// they are not passed in
+            }
 	    else if(line.matches("^\\s*endsection:\\s*\\S+")){
 		// ignore subsection info
             }