switching the json library according to request from Olivier Sallou

andreasprlic · andreasprlic · commit be3f49a8c57e · 2012-05-30T16:03:27.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9666 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-ws/pom.xml b/biojava3-ws/pom.xml
@@ -20,11 +20,11 @@
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
-
-		<dependency>
-			<groupId>org.json</groupId>
-			<artifactId>json</artifactId>
-			<version>20090211</version>
-		</dependency>
+   <dependency>
+            <groupId>net.sf.json-lib</groupId>
+            <artifactId>json-lib</artifactId>
+            <version>2.3</version>
+            <classifier>jdk15</classifier>
+        </dependency>
 	</dependencies>
 </project>
diff --git a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
@@ -13,8 +13,8 @@
 import java.util.TreeSet;
 
 import org.biojava3.core.sequence.ProteinSequence;
-import org.json.JSONArray;
-import org.json.JSONObject;
+import net.sf.json.JSONArray;
+import net.sf.json.JSONObject;
 
 
 /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
@@ -102,14 +102,14 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
 		try {
-			JSONObject json = new JSONObject(result.toString());
+			JSONObject json =  JSONObject.fromObject(result.toString());
 
 			JSONObject hmresults = json.getJSONObject("results");
 
 
 			JSONArray hits = hmresults.getJSONArray("hits");
 
-			for(int i =0 ; i < hits.length() ; i++){
+			for(int i =0 ; i < hits.size() ; i++){
 				JSONObject hit = hits.getJSONObject(i);
 				//System.out.println("hit: "+ hit);
 
@@ -128,7 +128,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 				JSONArray hmmdomains = hit.getJSONArray("domains");
 
 				SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
-				for ( int j= 0 ; j < hmmdomains.length() ; j++){
+				for ( int j= 0 ; j < hmmdomains.size() ; j++){
 					JSONObject d = hmmdomains.getJSONObject(j);
 					//System.out.println(d);
 					Integer is_reported = getInteger(d.get("is_reported"));
