[med-svn] r19917 - trunk/packages/biojava4-live/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2015-08-12 07:42:42 +0000 (Wed, 12 Aug 2015)
New Revision: 19917

Modified:
   trunk/packages/biojava4-live/trunk/debian/patches/fix_import
   trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
Log:
fix fuzz in patches

Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_import
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_import	2015-08-12 07:39:10 UTC (rev 19916)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_import	2015-08-12 07:42:42 UTC (rev 19917)
@@ -5,9 +5,9 @@
 Forwarded: no
 --- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
 +++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
-@@ -39,6 +39,13 @@
- import java.io.InputStream;
- import java.io.UnsupportedEncodingException;
+@@ -44,6 +44,13 @@
+ import org.biojava.nbio.structure.io.FastaStructureParser;
+ import org.biojava.nbio.structure.io.StructureSequenceMatcher;
  
 +import org.biojava.nbio.structure.StructureException;
 +import org.biojava.nbio.structure.Structure;

Modified: trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json	2015-08-12 07:39:10 UTC (rev 19916)
+++ trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json	2015-08-12 07:42:42 UTC (rev 19917)
@@ -19,7 +19,7 @@
  import org.biojava.nbio.core.sequence.ProteinSequence;
  
  import java.io.*;
-@@ -118,15 +120,13 @@
+@@ -133,15 +135,13 @@
  
  		SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
  		try {
@@ -39,7 +39,7 @@
  				//System.out.println("hit: "+ hit);
  
  				HmmerResult hmmResult = new HmmerResult();
-@@ -150,11 +150,11 @@
+@@ -166,11 +166,11 @@
  				hmmResult.setPvalue((Double)hit.get("pvalue"));
  				hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
  
@@ -51,5 +51,5 @@
 -					JSONObject d = hmmdomains.getJSONObject(j);
 +					JSONObject d = (JSONObject) hmmdomains.get(j);
  					//System.out.println(d);
- 					Integer is_reported = getInteger(d.get("is_reported"));
- 					if ( is_reported != 1) {
+ 					Integer is_included = getInteger(d.get("is_included"));
+ 					if ( is_included == 0) {