[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Thu Dec  6 18:46:34 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv31420/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyComplexBuilder.java 
Log Message:
Better non-default registry support, regex sub pattern fix
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyComplexBuilder.java,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java	2007/08/01 18:15:46	1.12
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java	2007/12/06 23:46:34	1.13
@@ -172,7 +172,7 @@
 	if(mobyDataType.getName().equals("Object")){
 	    mobyObj = new MobyDataObject("", SeahawkOptions.getRegistry());
 	}
-	else if(mobyDataType.inheritsFrom(MobyDataBytes.BASE64_DATATYPE)){
+	else if(mobyDataType.inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, SeahawkOptions.getRegistry()))){
 	    mobyObj = new MobyDataBytes("", (String) null);
 	    mobyObj.setDataType(mobyDataType);
 	}
@@ -286,9 +286,9 @@
 	    for(String result: results){
 		
 		if(PrimitiveTypes.isPrimitive(dataTypeName) ||
-		   MobyDataType.getDataType(dataTypeName, SeahawkOptions.getRegistry()).inheritsFrom(MobyDataBytes.BASE64_DATATYPE)){
+		   MobyDataType.getDataType(dataTypeName, SeahawkOptions.getRegistry()).inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, SeahawkOptions.getRegistry()))){
 		    ((MobyDataComposite) mobyObj).put(memberName, 
-						      MobyDataObject.createInstanceFromString(dataTypeName, result));
+						      MobyDataObject.createInstanceFromString(dataTypeName, result, SeahawkOptions.getRegistry()));
 		}
 		else{
 		    // Recursively call the object creator for complex members
@@ -448,7 +448,7 @@
 		}
 	    }
 	    // $# substitution in a string, considerably simpler!
-	    else if(result.matches("\\A.*?\\$"+j+"(?:\\D.*)?\\z")){
+	    else if(result.indexOf("$"+j) != -1){
 		String varValue = match.group(j);
 		if(whitespaceMode == null){
 		    // do nothing
@@ -541,7 +541,7 @@
 		    String value = xpath.evaluate(expr, result);
 
 		    ((MobyDataComposite) mobyObj).put(memberName, 
-						      MobyDataObject.createInstanceFromString(children[i].getDataTypeName(), value));
+						      MobyDataObject.createInstanceFromString(children[i].getDataTypeName(), value, SeahawkOptions.getRegistry()));
 		}
 	    }
 	}