[med-svn] [giira] 04/04: Consistent naming of patches; refreshed patch

[Andreas Tille]

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

tille pushed a commit to branch master
in repository giira.

commit b6617fba86d8f5657895da9697b9d316770d112c
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 10 13:47:14 2014 +0100

    Consistent naming of patches; refreshed patch
---
 debian/patches/fix_non-ascii_characters.patch                |  6 +++---
 .../patches/{remove_cplex_code => remove_cplex_code.patch}   | 12 ++++++------
 debian/patches/series                                        |  2 +-
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/debian/patches/fix_non-ascii_characters.patch b/debian/patches/fix_non-ascii_characters.patch
index aa84347..400d034 100644
--- a/debian/patches/fix_non-ascii_characters.patch
+++ b/debian/patches/fix_non-ascii_characters.patch
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at debian.org>
 Last-Updated: Sat, 08 Feb 2014 14:38:38 +0100
 Description: Remove non-ASII character from comment
 
---- giira.orig/src/types/Rna.java
-+++ giira/src/types/Rna.java
-@@ -17,7 +17,7 @@
+--- a/src/types/Rna.java
++++ b/src/types/Rna.java
+@@ -17,7 +17,7 @@ public class Rna {
  	
  	public double quality; 	  	
  
diff --git a/debian/patches/remove_cplex_code b/debian/patches/remove_cplex_code.patch
similarity index 93%
rename from debian/patches/remove_cplex_code
rename to debian/patches/remove_cplex_code.patch
index 2fce17d..d7821df 100644
--- a/debian/patches/remove_cplex_code
+++ b/debian/patches/remove_cplex_code.patch
@@ -8,7 +8,7 @@ Last-Updated: 2014-02-08
 Forwarded: no
 --- a/src/geneFinder/ReadInParameters_GeneFinder.java
 +++ b/src/geneFinder/ReadInParameters_GeneFinder.java
-@@ -242,9 +242,8 @@
+@@ -242,9 +242,8 @@ public class ReadInParameters_GeneFinder
  						GeneFinder.useGLPK = true;
  						inputText += "Using glpk for ambiguous read optimization.\n";
  					} else{
@@ -20,7 +20,7 @@ Forwarded: no
  					}
  				} else if(arg.equals("-mem")){
  					GeneFinder.memForCplex = Integer.parseInt(args[i+1]);			
-@@ -376,7 +375,8 @@
+@@ -376,7 +375,8 @@ public class ReadInParameters_GeneFinder
  			GeneFinder.noAmbiOpti = false;
  		}
  		if(!foundOptiMethod){
@@ -30,7 +30,7 @@ Forwarded: no
  		}
  		if(!foundSolveOn){
  			GeneFinder.optiSolve = true;
-@@ -458,8 +458,6 @@
+@@ -462,8 +462,6 @@ public class ReadInParameters_GeneFinder
  				" \n -haveSam [samfileName]: if a sam file already exists, provide the name, else a mapping is performed. NOTE: the sam file has to be sorted according to read names! \n" +
  				" \n -nT [numberThreads] : specify the maximal number of threads that are allowed to be used, DEFAULT: 1 \n" +
  				" \n -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat \n" +
@@ -50,7 +50,7 @@ Forwarded: no
  import java.io.*;
  import java.util.HashMap;
  import java.util.Map;
-@@ -377,47 +374,6 @@
+@@ -377,47 +374,6 @@ public class OptimizeAmbis {
  	
  	public static void solveMaxFlowWithCPLEX(int numMulti){
  		
@@ -100,7 +100,7 @@ Forwarded: no
  	/*
 --- a/src/geneFinder/Operon_LP.java
 +++ b/src/geneFinder/Operon_LP.java
-@@ -9,8 +9,6 @@
+@@ -9,8 +9,6 @@ package geneFinder;
   *
   */
  
@@ -109,7 +109,7 @@ Forwarded: no
  
  import java.io.*;
  import java.util.Vector;
-@@ -257,21 +255,6 @@
+@@ -257,21 +255,6 @@ public class Operon_LP {
  
  	public static void solveOperonLPWithCPLEX(){
  
diff --git a/debian/patches/series b/debian/patches/series
index e6b92ab..0b13371 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-remove_cplex_code
+remove_cplex_code.patch
 fix_non-ascii_characters.patch

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