[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Jan  7 17:07:45 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv15373/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Added more try blocks for pattern matching
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2007/12/17 18:37:55	1.18
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2008/01/07 22:07:45	1.19
@@ -613,19 +613,23 @@
 	    MobyComplexBuilder rule = regexMap.get(pattern);
 	    if(targetDataType == null ||
 	       rule.getDataType().inheritsFrom(targetDataType)){
-		Matcher matcher = pattern.matcher(textData);
-
-		while(matcher.find()){
-		    try{
-			MobyDataObject mobyObj = rule.apply(matcher);
-			if(mobyObj != null){
-			    objectVector.add(mobyObj);		
+		try{
+		    Matcher matcher = pattern.matcher(textData);
+		    
+		    while(matcher.find()){
+			try{
+			    MobyDataObject mobyObj = rule.apply(matcher);
+			    if(mobyObj != null){
+				objectVector.add(mobyObj);		
+			    }
+			}
+			catch(MobyException me){
+			    System.err.println("Could not build Moby object from match:" + me);
+			    me.printStackTrace();
 			}
 		    }
-		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match:" + me);
-			me.printStackTrace();
-		    }
+		} catch(Throwable t){  // Principally stack overflows
+		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text");
 		}
 	    }
 	}
@@ -770,20 +774,24 @@
 		    rawDataAsString = bytesToString(rawData);
 		    //System.err.println("Start of data is " + rawDataAsString.substring(0, 4));
 		}
-		Matcher matcher = pattern.matcher(rawDataAsString);
-
-		while(matcher.find()){
-		    //System.err.println("Found match for binary data");
-		    try{
-			MobyDataObject mobyObj = rule.apply(matcher, rawData);
-			if(mobyObj != null){
-			    objectVector.add(mobyObj);		
+		try{
+		    Matcher matcher = pattern.matcher(rawDataAsString);
+		    
+		    while(matcher.find()){
+			//System.err.println("Found match for binary data");
+			try{
+			    MobyDataObject mobyObj = rule.apply(matcher, rawData);
+			    if(mobyObj != null){
+				objectVector.add(mobyObj);		
+			    }
+			}
+			catch(MobyException me){
+			    System.err.println("Could not build Moby object from match:" + me);
+			    me.printStackTrace();
 			}
 		    }
-		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match:" + me);
-			me.printStackTrace();
-		    }
+		} catch(Throwable t){ // Principally stack overflows
+		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to binary data");
 		}
 	    }
 	}
@@ -834,21 +842,25 @@
 	Iterator regex_keys = regexMap.keySet().iterator();
 	while(regex_keys.hasNext()){ //map still has untraversed regex entry to test
 	    Pattern pattern = (Pattern) regex_keys.next();
-	    Matcher matcher = pattern.matcher(textData);
-
-	    while(matcher.find()){
-		MobyComplexBuilder rule = (MobyComplexBuilder) regexMap.get(pattern);
-
-		try{
-		    MobyDataObject mobyObj = rule.apply(matcher, bytes);
-		    if(mobyObj != null){
-			objectVector.add(mobyObj);		
+	    try{
+		Matcher matcher = pattern.matcher(textData);
+		
+		while(matcher.find()){
+		    MobyComplexBuilder rule = (MobyComplexBuilder) regexMap.get(pattern);
+		    
+		    try{
+			MobyDataObject mobyObj = rule.apply(matcher, bytes);
+			if(mobyObj != null){
+			    objectVector.add(mobyObj);		
+			}
+		    }
+		    catch(MobyException me){
+			System.err.println("Could not build Moby object from match:" + me);
+			me.printStackTrace();
 		    }
 		}
-		catch(MobyException me){
-		    System.err.println("Could not build Moby object from match:" + me);
-		    me.printStackTrace();
-		}
+	    }catch(Throwable t){ // Principally stack overflows
+		System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary");
 	    }
 	}