[med-svn] [biojava4-live] 02/05: Merge tag 'upstream/4.2.7+dfsg'

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository biojava4-live.

commit cf01cc3a865aab00225cf2ab65fe0de24461399a
Merge: 3d8f9d8 44affdc
Author: Olivier Sallou <osallou at debian.org>
Date:   Mon May 15 12:16:51 2017 +0000

    Merge tag 'upstream/4.2.7+dfsg'
    
    Upstream version 4.2.7+dfsg

 biojava-aa-prop/pom.xml                            |   6 +-
 biojava-alignment/pom.xml                          |   6 +-
 biojava-core/pom.xml                               |   2 +-
 biojava-genome/pom.xml                             |   6 +-
 .../nbio/genome/util/ChromosomeMappingTools.java   | 387 ++++++---------------
 .../org/biojava/nbio/genome/TestGenomeMapping.java | 380 ++++++++++++++------
 biojava-integrationtest/pom.xml                    |   4 +-
 .../nbio/structure/test/StructureToolsTest.java    |  51 ++-
 biojava-modfinder/pom.xml                          |   4 +-
 biojava-ontology/pom.xml                           |   2 +-
 biojava-phylo/pom.xml                              |   4 +-
 biojava-protein-disorder/pom.xml                   |   4 +-
 biojava-sequencing/pom.xml                         |   4 +-
 biojava-structure-gui/pom.xml                      |   6 +-
 biojava-structure/pom.xml                          |   6 +-
 .../main/java/org/biojava/nbio/structure/Calc.java |   7 +-
 .../org/biojava/nbio/structure/NucleotideImpl.java |  33 +-
 .../biojava/nbio/structure/asa/AsaCalculator.java  |  12 +-
 .../structure/symmetry/core/HelixAxisAligner.java  |  11 +-
 .../structure/symmetry/core/PermutationGroup.java  |   8 +-
 .../symmetry/core/RotationAxisAligner.java         |  13 +-
 .../structure/symmetry/core/RotationGroup.java     |   8 +-
 .../structure/symmetry/core/RotationSolver.java    | 189 +++++++---
 .../nbio/structure/symmetry/core/Subunits.java     |   6 +
 .../symmetry/geometry/IcosahedralSampler.java      |  17 +-
 .../structure/symmetry/geometry/SphereSampler.java |  48 ++-
 biojava-survival/pom.xml                           |   2 +-
 biojava-ws/pom.xml                                 |   4 +-
 .../org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java |  41 +--
 pom.xml                                            |   4 +-
 30 files changed, 742 insertions(+), 533 deletions(-)

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