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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
Last-Updated: 2012-12-02
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ b/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 org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.JSONValue;
+
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -136,15 +138,13 @@
SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
try {
- JSONObject json = JSONObject.fromObject(result.toString());
-
- JSONObject hmresults = json.getJSONObject("results");
-
+ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
+ 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 @@
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;
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