Subject: ASCII error in pbuilder
Description: unmappable character for encoding ASCII
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2012-12-05
Forwarded: yes
Bug: http://code.google.com/p/forester/issues/detail?id=1
--- a/biojava-forester/src/main/java/org/forester/test/Test.java
+++ b/biojava-forester/src/main/java/org/forester/test/Test.java
@@ -1310,7 +1310,7 @@
                 return false;
             }
             if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
-                    .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+                    .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) {
                 return false;
             }
             if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java
@@ -162,7 +162,6 @@
 
     /**
      * Returns the TM-Score for two superimposed sets of coordinates
-     * Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
      * @param x coordinate set 1
      * @param y coordinate set 2
      * @param lengthNative total length of native sequence
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -36,7 +36,6 @@
     /**
      * Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits
      * 
-     * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
      * @param subunits subunits to be scored
      * @param transformation transformation matrix
      * @param permutations permutation that determines which subunits are superposed
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
@@ -30,7 +30,6 @@
 /**
  * A chain, a start residue, and an end residue.
  *
- * Also stores a length. Because of insertion codes, this length is not necessarily {@code end − start}.
  */
 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();
 
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
@@ -74,7 +74,7 @@
  * immutable Annotation instances that are built from scratch each time.
  * @author  Matthew Pocock
  * @author <a href="mailto:kdj@sanger.ac.uk">Keith James</a> (docs).
- * @author  Kalle N�slund (docs)
+ * @author  Kalle Nslund (docs)
  * @see org.biojavax.RichAnnotatable
  * @since 1.0
  */
--- a/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
@@ -57,11 +57,11 @@
 			2WPD has 2 local symmetries.
 
 			Other examples with a single local symmetry are:
-			4F88 – local C8
-			1LTI – local C5
-			2W6E – local C3
-			2LXC – local C2
-			3OE7 – local C3
+			4F88 - local C8
+			1LTI - local C5
+			2W6E - local C3
+			2LXC - local C2
+			3OE7 - local C3
 
 			Local Pseudosymmetry, structure only
 
