[med-svn] [biojava4-live] 04/05: update patch for new release

[Olivier Sallou]

This is an automated email from the git hooks/post-receive script.

osallou pushed a commit to branch master
in repository biojava4-live.

commit 444f2ed80ea6a31656e0b9b9941654260701730a
Author: Olivier Sallou <osallou at debian.org>
Date:   Mon May 15 12:25:14 2017 +0000

    update patch for new release
---
 debian/patches/use_simple_json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/debian/patches/use_simple_json b/debian/patches/use_simple_json
index fb6dea9..c5633a0 100644
--- a/debian/patches/use_simple_json
+++ b/debian/patches/use_simple_json
@@ -17,9 +17,9 @@ Last-Updated: 2012-12-02
 +import org.json.simple.JSONValue;
 +
  import org.biojava.nbio.core.sequence.ProteinSequence;
- 
- import java.io.*;
-@@ -132,15 +134,13 @@
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+@@ -136,15 +138,13 @@
  
  		SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
  		try {
@@ -36,10 +36,10 @@ Last-Updated: 2012-12-02
  			for(int i =0 ; i < hits.size() ; i++){
 -				JSONObject hit = hits.getJSONObject(i);
 +				JSONObject hit = (JSONObject) hits.get(i);
- 				//System.out.println("hit: "+ hit);
  
  				HmmerResult hmmResult = new HmmerResult();
-@@ -165,11 +165,11 @@
+ 
+@@ -168,11 +168,11 @@
  				hmmResult.setPvalue((Double)hit.get("pvalue"));
  				hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
  
@@ -50,6 +50,6 @@ Last-Updated: 2012-12-02
  				for ( int j= 0 ; j < hmmdomains.size() ; j++){
 -					JSONObject d = hmmdomains.getJSONObject(j);
 +					JSONObject d = (JSONObject) hmmdomains.get(j);
- 					//System.out.println(d);
  					Integer is_included = getInteger(d.get("is_included"));
  					if ( is_included == 0) {
+ 						continue;

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/biojava4-live.git