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);
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