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#505 switching to https for all NCBI traffic - #525

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josemduarte merged 7 commits into
biojava:masterfrom
andreasprlic:master
Jul 4, 2016
Merged

#505 switching to https for all NCBI traffic#525
josemduarte merged 7 commits into
biojava:masterfrom
andreasprlic:master

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@andreasprlic

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* 'master' of github.com:biojava/biojava:
  [maven-release-plugin]prepare for next development iteration
  [maven-release-plugin]prepare release biojava-5.0.0-alpha5
  Added some tests on the structures.
  Fix to add chemComp info for the Basic MMTF test.
  A test that round trips mmtf files Fixes to do with chemcomp behaviour for seqRes and normal Groups
  Fix for the MmtfStructureReader to handle altLoc being a null byte.
  Added myself to the developers list
* 'master' of github.com:biojava/biojava: (31 commits)
  Implement tests for new utility methods in sequence objects biojava#491
  Method for total gapped positions and coverage in aligned sequences
  Method for percentage of identity of a sequence pair biojava#491
  Include a second structure clustering after internal symmetry
  Simplify and rename Demo for Quaternary Symmetry in structure-gui
  Add a test for helical symmetry detection
  Port the ScanSymmetry script to the symmetry project
  Create an ENUM for the symmetry perception methods
  Adapt test for Quaternary Symmetry detection with same examples
  Complete refactoring of QuatSymmetryDetector into static methods
  Expand test on Subunit Clustering classes
  Replace the CombinationGenerator with a PowerSet generator
  Create a conversion method from List SubunitCluster to Subunits
  Refactor QuatSymmetryParameters to have only symmetry params
  Deprecate old Chain Clustering classes
  Implement and test for dividing SubunitClusters with internal symmetry
  Test for bio assemblies in Subunit Extractor
  Move Subunits back to the symmetry.core package
  Create static SubunitClusterer equivalent to ChainClusterer
  Create SubunitCluster class and test with methods to merge clusters
  ...
@andreasprlic andreasprlic added this to the BioJava 5.0.0 milestone Jun 30, 2016
@heuermh

heuermh commented Jun 30, 2016

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Commit d78ab0b seems unrelated, otherwise I'm +1

@andreasprlic

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ah yes, there were some other minor improvements in my branch which got pulled in by this. if you are +1, please just merge. These are just minor edits overall, as such no need to vote :-)

@josemduarte

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This addresses #522. It would need to be merged to bugfixes-4.2 branch too. Perhaps it's easier to merge this to the bugfixes branch first and then merge that one into master.

@andreasprlic

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I'll cherry pick this also to the bugfix branch (only the ncbi https commits, not secondary structure)

@josemduarte
josemduarte merged commit 2fca095 into biojava:master Jul 4, 2016
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3 participants