[med-svn] [biojava4-live] branch master updated (3d8f9d8 -> fb51eea)

[Olivier Sallou]

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

      from  3d8f9d8   upload new upstream 4.2.5
       new  44affdc   New upstream version 4.2.7+dfsg
       new  cf01cc3   Merge tag 'upstream/4.2.7+dfsg'
       new  81e599d   new upstream release 4.2.7+dfsg
       new  444f2ed   update patch for new release
       new  fb51eea   fix release

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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 +--
 debian/changelog                                   |   6 +
 debian/patches/use_simple_json                     |  12 +-
 pom.xml                                            |   4 +-
 32 files changed, 754 insertions(+), 539 deletions(-)

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