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Title: Commits · sroughley/biojava · GitHub

Open Graph Title: Commits · sroughley/biojava

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Description: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. - Commits · sroughley/biojava

Open Graph Description: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. - Commits · sroughley/biojava

X Description: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. - Commits · sroughley/biojava

Opengraph URL: https://github.com/sroughley/biojava

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Merge branch 'master' of https://sroughley@github.com/sroughley/biojava.git	https://github.com/sroughley/biojava/commit/1093220fda2076ccf96f7a9c1becf659dc93bc8b
	https://github.com/sroughley
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1093220	https://github.com/sroughley/biojava/commit/1093220fda2076ccf96f7a9c1becf659dc93bc8b
	https://github.com/sroughley/biojava/tree/1093220fda2076ccf96f7a9c1becf659dc93bc8b
Fixed DBRef#toPDB() method to give 80 characters line	https://github.com/sroughley/biojava/commit/07de4bb16ccfa2d4f0000d6e204c7e3510f9a80e
	https://github.com/sroughley
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	https://github.com/sroughley/biojava/tree/07de4bb16ccfa2d4f0000d6e204c7e3510f9a80e
Merge pull request #2 from biojava/master	https://github.com/sroughley/biojava/commit/a6ea21efd34b79ac3018855ea4289c60808dc2a5
	https://github.com/sroughley
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Modified PBBFileParser to ensure all lines are 80 chars prior to parsing	https://github.com/sroughley/biojava/commit/ab9f89f818586778e60e47b51753afae779883cb
	https://github.com/sroughley
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	https://github.com/sroughley/biojava/tree/ab9f89f818586778e60e47b51753afae779883cb
Merge pull request #328 from sroughley/master	https://github.com/sroughley/biojava/commit/76ae666d561e1e01cd237a40d1e817859baadace
	https://github.com/josemduarte
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	https://github.com/sroughley/biojava/tree/76ae666d561e1e01cd237a40d1e817859baadace
Modified StructureTools#getGroupsWithinShell method to return a Set not	https://github.com/sroughley/biojava/commit/e27e1ac9393b17ef72f0e52f1e7e6c0798188bc7
	https://github.com/sroughley
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	https://github.com/sroughley/biojava/tree/e27e1ac9393b17ef72f0e52f1e7e6c0798188bc7
Merge pull request #1 from biojava/master	https://github.com/sroughley/biojava/commit/ad9b7916b40d05c81a07c1757c91d0fed1a997b2
	https://github.com/sroughley
sroughley	https://github.com/sroughley/biojava/commits?author=sroughley
ad9b791	https://github.com/sroughley/biojava/commit/ad9b7916b40d05c81a07c1757c91d0fed1a997b2
	https://github.com/sroughley/biojava/tree/ad9b7916b40d05c81a07c1757c91d0fed1a997b2
cleanup	https://github.com/sroughley/biojava/commit/0012c5fc2e1ffc860330a29b1ab0286dd371b2d3
	https://github.com/andreasprlic
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0012c5f	https://github.com/sroughley/biojava/commit/0012c5fc2e1ffc860330a29b1ab0286dd371b2d3
	https://github.com/sroughley/biojava/tree/0012c5fc2e1ffc860330a29b1ab0286dd371b2d3
#326 test for issue and fix	https://github.com/sroughley/biojava/commit/f3fa8b021fd59a053aa164b10e0807ab0a20fc00
	https://github.com/andreasprlic
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	https://github.com/sroughley/biojava/tree/f3fa8b021fd59a053aa164b10e0807ab0a20fc00
Removing warnings.	https://github.com/sroughley/biojava/commit/73f9247767356c051d052c74f58e3face31d89f5
	https://github.com/sbliven
sbliven	https://github.com/sroughley/biojava/commits?author=sbliven
73f9247	https://github.com/sroughley/biojava/commit/73f9247767356c051d052c74f58e3face31d89f5
	https://github.com/sroughley/biojava/tree/73f9247767356c051d052c74f58e3face31d89f5
don;t use Java 8 specific method names	https://github.com/sroughley/biojava/commit/f66a7fa1453b437a96622d571fd38b0311561351
	https://github.com/andreasprlic
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	https://github.com/sroughley/biojava/tree/f66a7fa1453b437a96622d571fd38b0311561351
work around if ReducedChemCompProvider is getting used	https://github.com/sroughley/biojava/commit/7d49d52991b6d02a3a1d7912baafdffb8cf69f0f
	https://github.com/andreasprlic
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adding support for parsing sequence mismatched into Chain class	https://github.com/sroughley/biojava/commit/589e3cb71a6debc314e4d6dd01018fc2d590d95a
	https://github.com/andreasprlic
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additional test for parsing SIFTs files	https://github.com/sroughley/biojava/commit/7e4c98568b9cb4f430d4cea4db9ce0aac857dd66
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Updating maven plugin versions	https://github.com/sroughley/biojava/commit/90df5945a9869958c6f503f6abe798dd40edefb6
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	https://github.com/sroughley/biojava/tree/90df5945a9869958c6f503f6abe798dd40edefb6
Merge pull request #323 from sbliven/master	https://github.com/sroughley/biojava/commit/ba88655d467839f2b9e6132e473d7a1a35290395
	https://github.com/sbliven
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Fix #321. Optimized completeGroup() for large groups.	https://github.com/sroughley/biojava/commit/209f41d0f880c664bae9371df28c3558b0a93ef2
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Use random seed unless specified in CeSymm optimization	https://github.com/sroughley/biojava/commit/c0b629451f6040411832d23849ff67c5df0fa502
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Method to get the principal axis index from a RotationGroup	https://github.com/sroughley/biojava/commit/f2ebc2eae82b46ea7a39319c53e70bdbc46a30c3
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	https://github.com/sroughley/biojava/tree/f2ebc2eae82b46ea7a39319c53e70bdbc46a30c3
Fix bug when an empty alignment is produced in CeSymm	https://github.com/sroughley/biojava/commit/d365f3f5763bc15d1130f0dd80411e63dec1cb32
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	https://github.com/sroughley/biojava/tree/d365f3f5763bc15d1130f0dd80411e63dec1cb32
Merge branch 'master' of github.com:biojava/biojava	https://github.com/sroughley/biojava/commit/156a6e287de239dda7e034865a6e58d0e95272db
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#322 starting to add support for struct_ref_seq_dif category	https://github.com/sroughley/biojava/commit/1570e125b1e957e86be5506564cc6fdf0e738b6a
	https://github.com/andreasprlic
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Fix ArrayIndexOutOfBounds due to iterating over too-short proteins	https://github.com/sroughley/biojava/commit/d7133ca2db08d96f99eec3b25f04f8d85de738b1
	https://github.com/sbliven
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#320 updating API	https://github.com/sroughley/biojava/commit/a34b1bb2bdbcadc2b579fd5a2a16d526ef2224da
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setting timeout when talking to Hmmer server	https://github.com/sroughley/biojava/commit/70b00cbbe4294d5216bab779571e79f96abd58fa
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#320 updating API	https://github.com/sroughley/biojava/commit/81c43959efd82ed4eec225f0e9f50bc8b576e8d5
	https://github.com/andreasprlic
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81c4395	https://github.com/sroughley/biojava/commit/81c43959efd82ed4eec225f0e9f50bc8b576e8d5
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adding icon (for display e.g. in SourceTree)	https://github.com/sroughley/biojava/commit/be55ad246ee0a79a17c0dc892762d252488cf005
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	https://github.com/sroughley/biojava/tree/be55ad246ee0a79a17c0dc892762d252488cf005
Bond and SSBond now implemented as interfaces backed by BondImpl and SSBondImpl, respectively.	https://github.com/sroughley/biojava/commit/1b363093a5b3fa912edf117257ebd8288a829c16
	https://github.com/jacob-litman
jacob-litman	https://github.com/sroughley/biojava/commits?author=jacob-litman
1b36309	https://github.com/sroughley/biojava/commit/1b363093a5b3fa912edf117257ebd8288a829c16
	https://github.com/sroughley/biojava/tree/1b363093a5b3fa912edf117257ebd8288a829c16
Merge pull request #318 from sbliven/master	https://github.com/sroughley/biojava/commit/c04eb8889b437ba2c62c30b806680f15f77a63bd
	https://github.com/sbliven
sbliven	https://github.com/sroughley/biojava/commits?author=sbliven
c04eb88	https://github.com/sroughley/biojava/commit/c04eb8889b437ba2c62c30b806680f15f77a63bd
	https://github.com/sroughley/biojava/tree/c04eb8889b437ba2c62c30b806680f15f77a63bd
Merge branch 'itasser'	https://github.com/sroughley/biojava/commit/7ecb81e7cfc9ecef62f458688d8b74acc5319ca9
	https://github.com/sbliven
sbliven	https://github.com/sroughley/biojava/commits?author=sbliven
7ecb81e	https://github.com/sroughley/biojava/commit/7ecb81e7cfc9ecef62f458688d8b74acc5319ca9
	https://github.com/sroughley/biojava/tree/7ecb81e7cfc9ecef62f458688d8b74acc5319ca9
Change logger messages of CeSymm to info level	https://github.com/sroughley/biojava/commit/9f57459fc5d4af65e5b85fa014061868268be083
	https://github.com/lafita
lafita	https://github.com/sroughley/biojava/commits?author=lafita
9f57459	https://github.com/sroughley/biojava/commit/9f57459fc5d4af65e5b85fa014061868268be083
	https://github.com/sroughley/biojava/tree/9f57459fc5d4af65e5b85fa014061868268be083
Fix NullPointer bug in CeSymm	https://github.com/sroughley/biojava/commit/dbcf6f077583565f7c6b2ff8d539434cd33ccac4
	https://github.com/lafita
lafita	https://github.com/sroughley/biojava/commits?author=lafita
dbcf6f0	https://github.com/sroughley/biojava/commit/dbcf6f077583565f7c6b2ff8d539434cd33ccac4
	https://github.com/sroughley/biojava/tree/dbcf6f077583565f7c6b2ff8d539434cd33ccac4
Add all scores to non-optimized symmetry results	https://github.com/sroughley/biojava/commit/576c7664e9c5dddb322d55a4ddbbb8c3a73090f9
	https://github.com/lafita
lafita	https://github.com/sroughley/biojava/commits?author=lafita
576c766	https://github.com/sroughley/biojava/commit/576c7664e9c5dddb322d55a4ddbbb8c3a73090f9
	https://github.com/sroughley/biojava/tree/576c7664e9c5dddb322d55a4ddbbb8c3a73090f9
Fix small bug with short non-symmetric alignments	https://github.com/sroughley/biojava/commit/3e3ed52a78290323e4b399ddb628692787a3d95c
	https://github.com/lafita
lafita	https://github.com/sroughley/biojava/commits?author=lafita
3e3ed52	https://github.com/sroughley/biojava/commit/3e3ed52a78290323e4b399ddb628692787a3d95c
	https://github.com/sroughley/biojava/tree/3e3ed52a78290323e4b399ddb628692787a3d95c
Fix bug when result was not symmetric in CeSymm	https://github.com/sroughley/biojava/commit/a22d9acf8fa68ce3e0a59a0fe13be8006323421d
	https://github.com/lafita
lafita	https://github.com/sroughley/biojava/commits?author=lafita
a22d9ac	https://github.com/sroughley/biojava/commit/a22d9acf8fa68ce3e0a59a0fe13be8006323421d
	https://github.com/sroughley/biojava/tree/a22d9acf8fa68ce3e0a59a0fe13be8006323421d
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