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();
+
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