Author: osallou-guest Date: 2012-12-02 22:09:13 +0000 (Sun, 02 Dec 2012) New Revision: 12582
Modified: trunk/packages/biojava3/trunk/debian/changelog trunk/packages/biojava3/trunk/debian/get-orig-source trunk/packages/biojava3/trunk/debian/patches/use_simple_json Log: New upstream release Modified: trunk/packages/biojava3/trunk/debian/changelog =================================================================== --- trunk/packages/biojava3/trunk/debian/changelog 2012-12-02 18:09:59 UTC (rev 12581) +++ trunk/packages/biojava3/trunk/debian/changelog 2012-12-02 22:09:13 UTC (rev 12582) @@ -1,3 +1,12 @@ +biojava3-live (3.0.5-1) UNRELEASED; urgency=low + + * New upstream release + * Use forester 1.005 + + # Waiting for source availability of Forester in biojava3 download site. + + -- Olivier Sallou <[email protected]> Sun, 02 Dec 2012 22:35:09 +0100 + biojava3-live (3.0.4-2) unstable; urgency=low [ Olivier Sallou ] Modified: trunk/packages/biojava3/trunk/debian/get-orig-source =================================================================== --- trunk/packages/biojava3/trunk/debian/get-orig-source 2012-12-02 18:09:59 UTC (rev 12581) +++ trunk/packages/biojava3/trunk/debian/get-orig-source 2012-12-02 22:09:13 UTC (rev 12582) @@ -24,8 +24,8 @@ mkdir -p biojava3-forester/src/main/java cd biojava3-forester/src/main/java - wget http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955-sources.jar - jar xf forester-0.955-sources.jar + wget http://www.biojava.org/download/maven/org/forester/1.005/forester-1.005-sources.jar + jar xf forester-1.005-sources.jar find . -name *.class | xargs rm -f cd ../../../.. cd .. Modified: trunk/packages/biojava3/trunk/debian/patches/use_simple_json =================================================================== --- trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2012-12-02 18:09:59 UTC (rev 12581) +++ trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2012-12-02 22:09:13 UTC (rev 12582) @@ -2,7 +2,7 @@ Author: Olivier Sallou <[email protected]> Description: json.org library is not "free", use simple_json library and update according to API -Last-Updated: 2012-05-30 +Last-Updated: 2012-12-02 --- a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java +++ b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java @@ -10,36 +10,35 @@ 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; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.JSONValue; /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence. -@@ -102,15 +103,14 @@ +@@ -102,15 +103,13 @@ SortedSet<HmmerResult> results = new TreeSet<HmmerResult>(); try { -- JSONObject json = new JSONObject(result.toString()); +- JSONObject json = JSONObject.fromObject(result.toString()); + JSONObject json= (JSONObject) JSONValue.parse(result.toString()); + JSONObject hmresults = (JSONObject) json.get("results"); - JSONObject hmresults = json.getJSONObject("results"); - +- +- +- JSONArray hits = hmresults.getJSONArray("hits"); + JSONArray hits = (JSONArray) hmresults.get("hits"); -- 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); -+ for(int i =0 ; i < hits.size() ; i++){ + JSONObject hit = (JSONObject) hits.get(i); //System.out.println("hit: "+ hit); HmmerResult hmmResult = new HmmerResult(); -@@ -125,11 +125,11 @@ +@@ -134,11 +133,11 @@ hmmResult.setPvalue((Double)hit.get("pvalue")); hmmResult.setScore(Float.parseFloat((String)hit.get("score"))); @@ -47,9 +46,8 @@ + JSONArray hmmdomains = (JSONArray) hit.get("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); -+ for ( int j= 0 ; j < hmmdomains.size() ; j++){ + JSONObject d = (JSONObject) hmmdomains.get(j); //System.out.println(d); Integer is_reported = getInteger(d.get("is_reported")); _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
