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1. Commits on Jul 1, 2016

   • Update readme.md

     andreasprlic

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   • Cleanup - squid:S1858 - "toString()" should never be called on a String object

     

     Mohamed Ezzat

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   • pmd:InefficientStringBuffering - Inefficient String Buffering

     

     Mohamed Ezzat

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2. Commits on Jun 30, 2016

   • #505 switching to https for all NCBI utils traffic.

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   • #505 switching to https for all NCBI utils traffic.

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3. Commits on Jun 27, 2016

   • Normalize percentage of identity by the length without gaps #521

     lafita

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4. Commits on Jun 24, 2016

   • Implement tests for new utility methods in sequence objects #491

     lafita

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   • Method for total gapped positions and coverage in aligned sequences

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     lafita

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   • Method for percentage of identity of a sequence pair #491

     lafita

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5. Commits on Jun 16, 2016

   • squid:S2272 - "Iterator.next()" methods should throw "NoSuchElementException"

     

     Mohamed Ezzat

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6. Commits on Jun 15, 2016

   • [maven-release-plugin]prepare for next development iteration

     

     Jenkins

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   • [maven-release-plugin]prepare release biojava-5.0.0-alpha4

     

     Jenkins

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   • squid:S2063 - Comparators should be Serializable

     

     Mohamed Ezzat

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7. Commits on Jun 10, 2016

   • squid:S2130 - Parsing should be used to convert Strings to primitives

     

     Mohamed Ezzat

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8. Commits on Jun 9, 2016

   • Merge pull request #499 from DevFactory/release--primitives-should-not-be-boxed-just-for-String-conversion-fix-1

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9. Commits on Jun 5, 2016

   • squid:S2131 - Primitives should not be boxed just for String conversion

     

     Mohamed Ezzat

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10. Commits on Jun 4, 2016

    • squid:S1197 - Array designators should be on the type, not the variable

      

      Mohamed Ezzat

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11. Commits on Jun 3, 2016

    • squid:S1125 - Literal boolean values should not be used in condition expressions

      

      Mohamed Ezzat

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12. Commits on Mar 10, 2016

    • [maven-release-plugin] prepare for next development iteration

      andreasprlic

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    • [maven-release-plugin] prepare release biojava-4.2.0

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    • Running spacestotabs on recent changes

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13. Commits on Mar 9, 2016

    • Removing unnecessary casts

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    • More whitespace fixes

      sbliven

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    • Removing unused imports

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    • Automatically adding missing @Override

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    • Converting initial spaces to tabs.

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      sbliven

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    • Removing template messages

      sbliven

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    • Remove trailing whitespace globally from .java files

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      sbliven

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    • Running addlicense.sh

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14. Commits on Mar 7, 2016

    • Make classes serializable for Spark

      abradle

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    • Make classes serializable for Spark

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    • Make classes serializable for Spark

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    • Make classes serializable for Spark

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    • Make classes serializable for Spark

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    • Updates to make serializable for Spark

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