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1. Commits on Sep 8, 2017

   • Fixing phosphosite urls and changing default url timeout to 30s

     josemduarte

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2. Commits on Aug 9, 2017

   • fixed minor issue with lack of this keyword, re-ran tests

     

     luke czapla

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   • made max values non-static and created final DEFAULT constants

     

     luke czapla

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   • Renamed MaxStagger (etc.) to maxStagger (etc.)

     

     luke czapla

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   • Subclasses not serializable

     

     luke czapla

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3. Commits on Aug 6, 2017

   • Structure object unmarked as transient for serialization

     

     luke czapla

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4. Commits on Aug 5, 2017

   • Merge remote-tracking branch 'upstream/master'

     Show description for ff49ad2
     

     luke czapla

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5. Commits on Aug 3, 2017

   • Merge branch 'master' of github.com:biojava/biojava into serialize

     lafita

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6. Commits on Aug 2, 2017

   • Fixing test after PDB v5 remediation

     josemduarte

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7. Commits on Jul 31, 2017

   • getters and setters all have full sentence JavaDoc

     

     luke czapla

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   • removed added * import

     

     luke czapla

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   • Full sentence revision of all JavaDoc and addition of separate error checking method

     

     luke czapla

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     luke czapla

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8. Commits on Jul 28, 2017

   • and the other files

     

     luke czapla

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     luke czapla

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   • fixed nomenclature for constants

     

     luke czapla

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     luke czapla

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   • Add a more complete check to structure serialization test

     lafita

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   • Make the secondary structure objects serializable

     lafita

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9. Commits on Jul 27, 2017

   • JavaDoc

     

     luke czapla

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     luke czapla

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10. Commits on Jul 26, 2017

    • Style changes

      

      luke czapla

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      luke czapla

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    • removed SNAPSHOT from since annotation

      

      luke czapla

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      luke czapla

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    • Serialization support for BasePairParameters class

      

      luke czapla

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      luke czapla

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    • final tests using getLength() and others

      

      luke czapla

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      luke czapla

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    • Getters and setters for default settings

      

      luke czapla

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      luke czapla

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    • Proposed revision

      

      luke czapla

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      luke czapla

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11. Commits on Jul 25, 2017

    • just minor forgotten exception line

      

      luke czapla

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      luke czapla

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    • Added author line and other suggestions

      

      luke czapla

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      luke czapla

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    • Added new getters and refined tests

      

      luke czapla

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    • Added new getters and refined tests

      

      luke czapla

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12. Commits on Jul 24, 2017

    • All classes moved to have an analyze() method and toString() for printing

      

      luke czapla

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13. Commits on Jul 23, 2017

    • Updated tests

      

      luke czapla

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    • switched from SeqRes to Atom seuqence and groups

      

      luke czapla

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    • Improved the twist calculation to much greater accuracy

      

      luke czapla

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14. Commits on Jul 22, 2017

    • finding base pairs between the same strand for hairpins

      

      luke czapla

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15. Commits on Jul 21, 2017

    • Test fix

      

      luke czapla

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    • Moved base pair code into new package basepairs

      

      luke czapla

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    • Made test use no println, and class use Logger

      

      luke czapla

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