Subject: use simple_json library
Author: Olivier Sallou <osallou@debian.org>
Description: json.org library is not "free", use simple_json
 library and update according to API
 .
 [ Gilles Filippini <pini@debian.org> ]
 Patche updated to migrate away from deprecated json-simple 1.x classes
 See json-simple 2.0.0 changelog:
 > * Deprecated JSONParse and JSONValue in favor of Jsoner.
 > * Deprecated JSONStreamAware and JSONAware in favor of Jsonable.
 > * Deprecated JSONObject in favor of JsonObject.
 > * Deprecated JSONArray in favor of JsonArray.
 .
 This patch now uses the new json-simple Json* classes. It is compatible
 with both 2.x and 3.x json-simple releases, with a few ajustments
 regarding backward incompatible changes in json-simple 3.x:
 - The package name, changed to com.github.cliftonlabs.json_simple
 This change is handled using place-holders @JSON_SIMPLE_PACKAGE@ which
 are substituted at build time by debian/rules.
 .
 With this trick the package is compatible with json-simple 2.x and 3.x.
Last-Updated: 2020-05-15
Index: biojava4-live-4.2.12+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
===================================================================
--- biojava4-live-4.2.12+dfsg.orig/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ biojava4-live-4.2.12+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -20,8 +20,10 @@
  */
 package org.biojava.nbio.ws.hmmer;
 
-import net.sf.json.JSONArray;
-import net.sf.json.JSONObject;
+import @JSON_SIMPLE_PACKAGE@.JsonArray;
+import @JSON_SIMPLE_PACKAGE@.JsonObject;
+import @JSON_SIMPLE_PACKAGE@.Jsoner;
+
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -136,15 +138,13 @@ public class RemoteHmmerScan implements
 
 		SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
 		try {
-			JSONObject json =  JSONObject.fromObject(result.toString());
-
-			JSONObject hmresults = json.getJSONObject("results");
-
+			JsonObject json= Jsoner.deserialize(result.toString(), (JsonObject) null);
+			JsonObject hmresults = (JsonObject) json.get("results");
 
-			JSONArray hits = hmresults.getJSONArray("hits");
+			JsonArray hits = (JsonArray) hmresults.get("hits");
 
 			for(int i =0 ; i < hits.size() ; i++){
-				JSONObject hit = hits.getJSONObject(i);
+				JsonObject hit = (JsonObject) hits.get(i);
 
 				HmmerResult hmmResult = new HmmerResult();
 
@@ -168,11 +168,11 @@ public class RemoteHmmerScan implements
 				hmmResult.setPvalue((Double)hit.get("pvalue"));
 				hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
 
-				JSONArray hmmdomains = hit.getJSONArray("domains");
+				JsonArray hmmdomains = (JsonArray) hit.get("domains");
 
 				SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
 				for ( int j= 0 ; j < hmmdomains.size() ; j++){
-					JSONObject d = hmmdomains.getJSONObject(j);
+					JsonObject d = (JsonObject) hmmdomains.get(j);
 					Integer is_included = getInteger(d.get("is_included"));
 					if ( is_included == 0) {
 						continue;