[med-svn] r12582 - in trunk/packages/biojava3/trunk/debian: . patches

[olivier sallou]

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 <osallou at debian.org>  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 <osallou at debian.org>
 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"));