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Title: History for biojava-genome/src/main - biojava/biojava · GitHub

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Description: :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data. - History for biojava-genome/src/main - biojava/biojava

Open Graph Description: :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data. - History for biojava-genome/src/main - biojava/biojava

X Description: :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data. - History for biojava-genome/src/main - biojava/biojava

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Fix issue s1319 Declarations should use Java collection interfaces on biojava-corehttps://github.com/biojava/biojava/commit/1ae6b52630282eba2079b5764218f5420c1b12b5
https://github.com/jlerbsc
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https://github.com/biojava/biojava/tree/1ae6b52630282eba2079b5764218f5420c1b12b5
Fix sonar issue S2293 Replace the type specification in this constructor call with the diamond operator ('<>')https://github.com/biojava/biojava/commit/b18212163e0fd9ff56da13ef258005b7d0decced
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https://github.com/biojava/biojava/tree/b18212163e0fd9ff56da13ef258005b7d0decced
fix sonar issue 2629 Logging arguments should not require evaluationhttps://github.com/biojava/biojava/commit/1ac29b3fae37ab43b2316ea1c9901de33620c978
https://github.com/jlerbsc
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fix: issue #1081 Sonar S1132 Strings literals should be placed on the left side when checking for equalityhttps://github.com/biojava/biojava/commit/ac75f31259e94a6d9d417e7faa2eaf2598c56f1a
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Merge remote-tracking branch 'origin/master'https://github.com/biojava/biojava/commit/4796663617b917ed463d58eb30fa8cb8371f4110
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Sonar S2129 Constructors should not be used to instantiate 'String', 'BigInteger', 'BigDecimal' and primitive-wrapper classes (Issue #1066)https://github.com/biojava/biojava/commit/4a1863d66121687b67229ed1ca1fd7466267663d
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Sonar S4973 '==' and '!=' should not be used when 'equals' is overridden #1052https://github.com/biojava/biojava/commit/caa57898c1da3ebe6e1710d00d3050502a013933
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Sonar S4973 '==' and '!=' should not be used when 'equals' is overridden #1052https://github.com/biojava/biojava/commit/963dc0125f188592c82699f49a519b9364e7a078
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Removing a utility tool that was really internal to biojava, but that was using external resources that are now gone.https://github.com/biojava/biojava/commit/0e47572ab6b66bf21f074edbe16c793eb775c6fe
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Add copy constructor to FastqBuilder.https://github.com/biojava/biojava/commit/02b0ece17db3dc6ace817c231ea0ae7998cfcc1b
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Collect to ArrayList rather than LinkedList.https://github.com/biojava/biojava/commit/1e59bb59883c3d2afe88671d60f48924fc3ece73
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Remove unused importhttps://github.com/biojava/biojava/commit/f8148e9953b07d53fdaabcfe5d5f3f7bebad292b
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Add GFF3Reader overload that accepts Pathhttps://github.com/biojava/biojava/commit/35594ef4d63cf32cb9c3fe2ee79bd16ba8577462
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Fixed impact of refactoring on genome modulehttps://github.com/biojava/biojava/commit/8040e3976f2f41a1e1671d8f347af12f3afa003e
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Manually fix cases of space indentation identation found byhttps://github.com/biojava/biojava/commit/5baab5ef23be72c8f109dd89abd9e5d5e9fb3e8f
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https://github.com/biojava/biojava/blob/5baab5ef23be72c8f109dd89abd9e5d5e9fb3e8f/biojava-genome/src/main
https://github.com/biojava/biojava/tree/5baab5ef23be72c8f109dd89abd9e5d5e9fb3e8f
Automatically convert spaces to tabshttps://github.com/biojava/biojava/commit/9ae2c4fe643cea3c207e2a3f81d2ac38dacea8a6
https://github.com/sbliven
sblivenhttps://github.com/biojava/biojava/commits?author=sbliven
9ae2c4fhttps://github.com/biojava/biojava/commit/9ae2c4fe643cea3c207e2a3f81d2ac38dacea8a6
https://github.com/biojava/biojava/blob/9ae2c4fe643cea3c207e2a3f81d2ac38dacea8a6/biojava-genome/src/main
https://github.com/biojava/biojava/tree/9ae2c4fe643cea3c207e2a3f81d2ac38dacea8a6
Remove trailing spaces from java fileshttps://github.com/biojava/biojava/commit/405b005c0ccd53f0900c2f9d168fd052d18281f7
https://github.com/sbliven
sblivenhttps://github.com/biojava/biojava/commits?author=sbliven
405b005https://github.com/biojava/biojava/commit/405b005c0ccd53f0900c2f9d168fd052d18281f7
https://github.com/biojava/biojava/blob/405b005c0ccd53f0900c2f9d168fd052d18281f7/biojava-genome/src/main
https://github.com/biojava/biojava/tree/405b005c0ccd53f0900c2f9d168fd052d18281f7
Merge branch 'bugfixes-4.2'https://github.com/biojava/biojava/commit/0501615a3106e54aa41216336f65b197bc03e50e
https://github.com/sbliven
sblivenhttps://github.com/biojava/biojava/commits?author=sbliven
0501615https://github.com/biojava/biojava/commit/0501615a3106e54aa41216336f65b197bc03e50e
https://github.com/biojava/biojava/blob/0501615a3106e54aa41216336f65b197bc03e50e/biojava-genome/src/main
https://github.com/biojava/biojava/tree/0501615a3106e54aa41216336f65b197bc03e50e
Merge pull request #749 from josemduarte/removeV4deprecationshttps://github.com/biojava/biojava/commit/763f7ecc28716071bc93b69e0aa2df51cbbe96da
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
763f7echttps://github.com/biojava/biojava/commit/763f7ecc28716071bc93b69e0aa2df51cbbe96da
https://github.com/biojava/biojava/blob/763f7ecc28716071bc93b69e0aa2df51cbbe96da/biojava-genome/src/main
https://github.com/biojava/biojava/tree/763f7ecc28716071bc93b69e0aa2df51cbbe96da
Add license to all fileshttps://github.com/biojava/biojava/commit/0e8c081c44098127953112c08bb39c01982b468f
https://github.com/sbliven
sblivenhttps://github.com/biojava/biojava/commits?author=sbliven
0e8c081https://github.com/biojava/biojava/commit/0e8c081c44098127953112c08bb39c01982b468f
https://github.com/biojava/biojava/blob/0e8c081c44098127953112c08bb39c01982b468f/biojava-genome/src/main
https://github.com/biojava/biojava/tree/0e8c081c44098127953112c08bb39c01982b468f
Removing deprecations from v4https://github.com/biojava/biojava/commit/9dbf83c0eb552dd89772d2829c007eed41cedf96
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
9dbf83chttps://github.com/biojava/biojava/commit/9dbf83c0eb552dd89772d2829c007eed41cedf96
https://github.com/biojava/biojava/blob/9dbf83c0eb552dd89772d2829c007eed41cedf96/biojava-genome/src/main
https://github.com/biojava/biojava/tree/9dbf83c0eb552dd89772d2829c007eed41cedf96
Added moved note and cleaned up unused variable and some docshttps://github.com/biojava/biojava/commit/a61fb7510130e679ffb22a3d7a3b2bec2e59a8e7
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
a61fb75https://github.com/biojava/biojava/commit/a61fb7510130e679ffb22a3d7a3b2bec2e59a8e7
https://github.com/biojava/biojava/blob/a61fb7510130e679ffb22a3d7a3b2bec2e59a8e7/biojava-genome/src/main
https://github.com/biojava/biojava/tree/a61fb7510130e679ffb22a3d7a3b2bec2e59a8e7
Merging sequencing module into genome module as per #536https://github.com/biojava/biojava/commit/59fd363a862706517fb4066b67c78ab2cc24d12d
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
59fd363https://github.com/biojava/biojava/commit/59fd363a862706517fb4066b67c78ab2cc24d12d
https://github.com/biojava/biojava/blob/59fd363a862706517fb4066b67c78ab2cc24d12d/biojava-genome/src/main
https://github.com/biojava/biojava/tree/59fd363a862706517fb4066b67c78ab2cc24d12d
Updating genenames.org url to httpshttps://github.com/biojava/biojava/commit/97ca0c1061babf21e2a562869f744d9595710767
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
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https://github.com/biojava/biojava/blob/97ca0c1061babf21e2a562869f744d9595710767/biojava-genome/src/main
https://github.com/biojava/biojava/tree/97ca0c1061babf21e2a562869f744d9595710767
Updating genenames.org url to httpshttps://github.com/biojava/biojava/commit/39d8c242e1190b2bdf9a3c14b67e4abcd36e72e1
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
39d8c24https://github.com/biojava/biojava/commit/39d8c242e1190b2bdf9a3c14b67e4abcd36e72e1
https://github.com/biojava/biojava/blob/39d8c242e1190b2bdf9a3c14b67e4abcd36e72e1/biojava-genome/src/main
https://github.com/biojava/biojava/tree/39d8c242e1190b2bdf9a3c14b67e4abcd36e72e1
improvementshttps://github.com/biojava/biojava/commit/3e2be54f32f5807c2c1fc99c81caac7683c06849
https://github.com/valasatava
valasatavahttps://github.com/biojava/biojava/commits?author=valasatava
3e2be54https://github.com/biojava/biojava/commit/3e2be54f32f5807c2c1fc99c81caac7683c06849
https://github.com/biojava/biojava/blob/3e2be54f32f5807c2c1fc99c81caac7683c06849/biojava-genome/src/main
https://github.com/biojava/biojava/tree/3e2be54f32f5807c2c1fc99c81caac7683c06849
Setter for chromosome coordinate systems: 0-based, 1-basedhttps://github.com/biojava/biojava/commit/b69ddfb7bd9a78199ae76c4430d2b5b7722613fb
https://github.com/valasatava
valasatavahttps://github.com/biojava/biojava/commits?author=valasatava
b69ddfbhttps://github.com/biojava/biojava/commit/b69ddfb7bd9a78199ae76c4430d2b5b7722613fb
https://github.com/biojava/biojava/blob/b69ddfb7bd9a78199ae76c4430d2b5b7722613fb/biojava-genome/src/main
https://github.com/biojava/biojava/tree/b69ddfb7bd9a78199ae76c4430d2b5b7722613fb
CDS length calculation bug fixhttps://github.com/biojava/biojava/commit/033d92e7fd2851157c8298c77b32ef811f36d2fe
https://github.com/valasatava
valasatavahttps://github.com/biojava/biojava/commits?author=valasatava
033d92ehttps://github.com/biojava/biojava/commit/033d92e7fd2851157c8298c77b32ef811f36d2fe
https://github.com/biojava/biojava/blob/033d92e7fd2851157c8298c77b32ef811f36d2fe/biojava-genome/src/main
https://github.com/biojava/biojava/tree/033d92e7fd2851157c8298c77b32ef811f36d2fe
Nexthttps://github.com/biojava/biojava/commits/biojava-7.2.5/biojava-genome/src/main?after=5d047ab428b176a437131d31171c7f779caa239e+34
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