[med-svn] r18674 - trunk/packages/biojava4-live/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2015-01-31 15:38:13 +0000 (Sat, 31 Jan 2015)
New Revision: 18674

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 14:33:26 UTC (rev 18673)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping	2015-01-31 15:38:13 UTC (rev 18674)
@@ -15,3 +15,33 @@
                  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);