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Speedup #30

Merged
merged 22 commits into from
Mar 28, 2017
Merged

Speedup #30

merged 22 commits into from
Mar 28, 2017

Commits on Feb 28, 2017

  1. Modified access to resource files so that it works on Windows and 

    hopefully every other OS.
    @altaite
    altaite committed Feb 28, 2017
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Commits on Mar 1, 2017

  1. Replaced Jackson by MessagePack parsing code from Jmol. Jackson remains 

    available by a switch in MessagePackSerialization.
    @altaite
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  2. Moving code from getNumBonds() to constructor results in 4-fold speedup 

    of BioJava Structure creation.
    @altaite
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  3. FLOAT64 is now parsed as double, which corresponds to what Jackson did. 

    Passed MessagePackTest.
    @altaite
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Commits on Mar 5, 2017

  1. Added a test comparing if results of Jackson and the new MessagePack 

    parser adopted from Jmol are identical.
    @altaite
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  2. Moved MessagePack test into mmtf-codec.

    @altaite
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Commits on Mar 6, 2017

  1. Version set to 1.05.

    @altaite
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Commits on Mar 9, 2017

  1. Renaming of mp package to quickmessagepackdeserialization.

    @altaite
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Commits on Mar 17, 2017

  1. Zipped resource pdb_entry_type.txt. Replaced few other 

    RuntimeExceptions by IOException and try with resources.
    @altaite
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Commits on Mar 18, 2017

  1. Replaced zip with gz. Also corrected the loading of file using URL, 

    previous was failing on Windows again. Going to use URL elsewhere 
too in the next commit.
    @altaite
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Commits on Mar 21, 2017

  1. Nicer code for reading text files as resources in gz. URL are used 

    whenever possible (simpler and more reliable), File left only when 
necessary for API tests.
    @altaite
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Commits on Mar 22, 2017

  1. Minor formatting changes and removal of dead code in comments.

    @altaite
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Commits on Mar 23, 2017

  1. Message Pack parsing code from Bob Hanson's Jmol simplified and moved… 

    … to one class.
    @altaite
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Commits on Mar 24, 2017

  1. PDB codes for testing now does not contain missing records (no codes … 

    …after 12/01/2016). Increased -Xmx for

testing from 1500 to 6000 MB because sometimes GC timeout occured in MessagePackTest. Improved comments on the MessagePack parser.
    @altaite
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Commits on Mar 25, 2017

  1. Correction of versions to 1.0.4-SNAPSHOT.

    @altaite
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Commits on Mar 26, 2017

  1. Better API for Lines utility.

    @altaite
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Commits on Mar 27, 2017

  1. Merge branch 'master' into speedup

    @altaite
    altaite authored Mar 27, 2017
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  2. Better API for Lines utility. Also number of tested structures 

    was corrected to reasonable number 10.
    @altaite
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  3. Merge origin/speedup into speedup

    @altaite
    altaite committed Mar 27, 2017
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Commits on Mar 28, 2017

  1. Replaced Exception for ParseException in MessagePack decoding.

    @altaite
    altaite committed Mar 28, 2017
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  2. More appropriate name for test.

    @altaite
    altaite committed Mar 28, 2017
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  3. More descriptive method names in ObjectTree.

    @altaite
    altaite committed Mar 28, 2017
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