[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Thu Apr 26 11:22:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv718/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Small method sig and doc updates
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2007/04/18 16:01:00	1.11
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2007/04/26 15:22:27	1.12
@@ -740,11 +740,11 @@
 	    return new MobyDataObject[0];
 	}
 
-	// Vector of moby objects we construct based on the xpath mappings found
+	// Vector of moby objects we construct based on the regex mappings found
 	Vector objectVector = new Vector(); 
 
 	Iterator regex_keys = regexMap.keySet().iterator();
-	while(regex_keys.hasNext()){ //map still has untraversed xpath entry to test
+	while(regex_keys.hasNext()){ //map still has untraversed regex entry to test
 	    Pattern pattern = (Pattern) regex_keys.next();
 	    Matcher matcher = pattern.matcher(textData);
 
@@ -771,29 +771,44 @@
      * Using the URL regular expression mappings that have been set up, 
      * maps a string to moby objects.  URL regexs are special because they are
      * flexible in the order in which query parameters are given.  They
-     * may also have requirements based on the hypertext linked.
+     * may also have requirements based on the hypertext linked. This method
+     * does not look at the contents of the URL, but rather the URL itself.
      */
     public MobyDataObject[] getMobyObjects(URL url){
-	return getMobyObjects(url, null);
+	return getMobyObjects(url, null, null);
     }
 
     public MobyDataObject[] getMobyObjects(URL url, String linkText){
+	return getMobyObjects(url, linkText, null);
+    }
+
+    public MobyDataObject[] getMobyObjects(URL url, MobyDataType targetDataType){
+	return getMobyObjects(url, null, targetDataType);
+    }
+
+    public MobyDataObject[] getMobyObjects(URL url, String linkText, MobyDataType targetDataType){
 	if(urlRegexMap.isEmpty()){
 	    System.out.println("The MOBY Client has not been provided any url regex->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 
-	// Vector of moby objects we construct based on the xpath mappings found
+	// Vector of moby objects we construct based on the regex mappings found
 	Vector objectVector = new Vector(); 
 
 	String urlString = url.toString();
 	Iterator url_regex_keys = urlRegexMap.keySet().iterator();
-	while(url_regex_keys.hasNext()){ // map still has untraversed xpath entry to test
+	while(url_regex_keys.hasNext()){ // map still has untraversed regex entry to test
 	    Pattern pattern = (Pattern) url_regex_keys.next();
+	    MobyComplexBuilder rule = (MobyComplexBuilder) urlRegexMap.get(pattern);
+
+	    // If we asked for a particular data type, make sure the rule can produce it before we
+	    // start to go matching it.
+	    if(targetDataType != null && !rule.getDataType().inheritsFrom(targetDataType)){
+		continue;
+	    }
 	    Matcher matcher = pattern.matcher(urlString);
 
 	    while(matcher.find()){
-		MobyComplexBuilder rule = (MobyComplexBuilder) urlRegexMap.get(pattern);
 
 		try{
 		    MobyDataObject mobyObj = rule.apply(matcher);