[med-svn] r18675 - trunk/packages/biojava4-live/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2015-01-31 15:48:29 +0000 (Sat, 31 Jan 2015)
New Revision: 18675

Modified:
   trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
Log:
fix ascii mapping

Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping	2015-01-31 15:38:13 UTC (rev 18674)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping	2015-01-31 15:48:29 UTC (rev 18675)
@@ -45,3 +45,31 @@
   */
  public class ResidueRangeAndLength extends ResidueRange {
  	private static final Logger logger = LoggerFactory.getLogger(ResidueRangeAndLength.class);
+--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
++++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
+@@ -29,13 +29,13 @@
+ import java.util.List;
+ 
+ /**
+- * Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
++ * Phosphosite is available under the PhosphoSitePlus is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
+  *
+  * http://www.phosphosite.org/staticDownloads.do
+  *
+- * Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
++ * Please acknowledge PhosphoSitePlus, www.phosphosite.org" at appropriate locations.
+  *
+- * Please cite : “Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.”.
++ * Please cite : "Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.".
+  *
+  (
+  *
+@@ -111,7 +111,7 @@
+     public void download(){
+ 
+         System.out.println("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: ");
+-        System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.");
++        System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70.");
+ 
+         File dir = getLocalDir();
+