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Title: Commits · JavaMuller/biojava · GitHub

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

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

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

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

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Merging from master to biojava-ffx integration branch.https://github.com/JavaMuller/biojava/commit/3fc00bef825002bbd835a175dba4328d840fd309
https://github.com/jacob-litman
jacob-litmanhttps://github.com/JavaMuller/biojava/commits?author=jacob-litman
3fc00behttps://github.com/JavaMuller/biojava/commit/3fc00bef825002bbd835a175dba4328d840fd309
https://github.com/JavaMuller/biojava/tree/3fc00bef825002bbd835a175dba4328d840fd309
Updated POMs in preparation for hosting as separate Maven repository; a few comments and log messages also got slightly refactored. Everything seems ready for public Biojava-FFX integration (with t…https://github.com/JavaMuller/biojava/commit/8fe919aa6f201793c41780a09b4f7b9c3d1f600d
8fe919ahttps://github.com/JavaMuller/biojava/commit/8fe919aa6f201793c41780a09b4f7b9c3d1f600d
https://github.com/JavaMuller/biojava/tree/8fe919aa6f201793c41780a09b4f7b9c3d1f600d
Merge remote-tracking branch 'upstream/master'https://github.com/JavaMuller/biojava/commit/df98f2ef4b69f977000400fcd011761afb1d0491
https://github.com/josemduarte
josemduartehttps://github.com/JavaMuller/biojava/commits?author=josemduarte
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https://github.com/JavaMuller/biojava/tree/df98f2ef4b69f977000400fcd011761afb1d0491
Merge pull request #311 from lafita/cesymmhttps://github.com/JavaMuller/biojava/commit/bd62ae259019ae9589b08d05557eaa5cf1d179fc
https://github.com/andreasprlic
andreasprlichttps://github.com/JavaMuller/biojava/commits?author=andreasprlic
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https://github.com/JavaMuller/biojava/tree/bd62ae259019ae9589b08d05557eaa5cf1d179fc
Merge pull request #312 from lafita/fix309https://github.com/JavaMuller/biojava/commit/63861777e66ae5abd5407f194fa41e408d789282
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
6386177https://github.com/JavaMuller/biojava/commit/63861777e66ae5abd5407f194fa41e408d789282
https://github.com/JavaMuller/biojava/tree/63861777e66ae5abd5407f194fa41e408d789282
Use C-alpha Atoms in AltLocs Testhttps://github.com/JavaMuller/biojava/commit/f2c25d57de9597b290d336523333aa8dba938810
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
f2c25d5https://github.com/JavaMuller/biojava/commit/f2c25d57de9597b290d336523333aa8dba938810
https://github.com/JavaMuller/biojava/tree/f2c25d57de9597b290d336523333aa8dba938810
Fix StructureToolsTest to pass according to changeshttps://github.com/JavaMuller/biojava/commit/2927b321308cc20008a4e8aa451359806cd1683e
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
2927b32https://github.com/JavaMuller/biojava/commit/2927b321308cc20008a4e8aa451359806cd1683e
https://github.com/JavaMuller/biojava/tree/2927b321308cc20008a4e8aa451359806cd1683e
Allow non-refined result, only self-alignmenthttps://github.com/JavaMuller/biojava/commit/6beb84973b8037383639b59393f95a9e30174071
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
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https://github.com/JavaMuller/biojava/tree/6beb84973b8037383639b59393f95a9e30174071
Fix demo issueshttps://github.com/JavaMuller/biojava/commit/90b44036d0c503d81478190f4fc836e8c5037d1c
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
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https://github.com/JavaMuller/biojava/tree/90b44036d0c503d81478190f4fc836e8c5037d1c
Crate Test for consistency in getting representative Atomshttps://github.com/JavaMuller/biojava/commit/edb9e7312263716e58fdb6385243407504c2da8f
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
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https://github.com/JavaMuller/biojava/tree/edb9e7312263716e58fdb6385243407504c2da8f
Make getRepresentative Atoms consistenthttps://github.com/JavaMuller/biojava/commit/b1bd53489399431df8f93df548fd31f6afda3580
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
b1bd534https://github.com/JavaMuller/biojava/commit/b1bd53489399431df8f93df548fd31f6afda3580
https://github.com/JavaMuller/biojava/tree/b1bd53489399431df8f93df548fd31f6afda3580
Fixing issue in getAlignedResIndex, now the mapping will work forhttps://github.com/JavaMuller/biojava/commit/7f1a7f3cb8cffd6ac710dbea36f032e8cbc45f51
https://github.com/josemduarte
josemduartehttps://github.com/JavaMuller/biojava/commits?author=josemduarte
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https://github.com/JavaMuller/biojava/tree/7f1a7f3cb8cffd6ac710dbea36f032e8cbc45f51
Add Demo for CeSymmhttps://github.com/JavaMuller/biojava/commit/e5cfa6b7ce4cc2fc30ea5f14899549c09fa77a7d
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
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https://github.com/JavaMuller/biojava/tree/e5cfa6b7ce4cc2fc30ea5f14899549c09fa77a7d
Port CeSymm for internal symmetry detection code to BioJavahttps://github.com/JavaMuller/biojava/commit/05c6c35753d305d0d828db73ffa56406a400a71f
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
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https://github.com/JavaMuller/biojava/tree/05c6c35753d305d0d828db73ffa56406a400a71f
fix for #306 - now checks provided URL if it contains the string ".cif" and switches to mmCif parsing accordingly.https://github.com/JavaMuller/biojava/commit/f9d0480604d5c6efa668de04d76ab19078ac10c4
https://github.com/andreasprlic
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https://github.com/JavaMuller/biojava/tree/f9d0480604d5c6efa668de04d76ab19078ac10c4
#308 adding a test that demonstrates that fetching mmCIF files from remote URLs is broken. Also tests for correct parsing of compressed files.https://github.com/JavaMuller/biojava/commit/66cfcdcc2e013e4c9d279656bb59dc04ea9afffe
https://github.com/andreasprlic
andreasprlichttps://github.com/JavaMuller/biojava/commits?author=andreasprlic
66cfcdchttps://github.com/JavaMuller/biojava/commit/66cfcdcc2e013e4c9d279656bb59dc04ea9afffe
https://github.com/JavaMuller/biojava/tree/66cfcdcc2e013e4c9d279656bb59dc04ea9afffe
Minor fixhttps://github.com/JavaMuller/biojava/commit/7cd71004e650164d5d15825f85a10cced119dcfd
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josemduartehttps://github.com/JavaMuller/biojava/commits?author=josemduarte
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Extended the interface-implementation paradigm to Bonds and SSBonds. Renamed chain.getParent() and chain.setParent() to chain.getStructure() and chain.setStructure() to deconflict with other APIs. …https://github.com/JavaMuller/biojava/commit/ffdc278c251092da01dca94f1891ab7c95753a6a
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https://github.com/JavaMuller/biojava/tree/ffdc278c251092da01dca94f1891ab7c95753a6a
Some cosmeticshttps://github.com/JavaMuller/biojava/commit/2a16a64ac7a33ea6f1ff0e97b124a4485acfeff3
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josemduartehttps://github.com/JavaMuller/biojava/commits?author=josemduarte
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Making tests less verbosehttps://github.com/JavaMuller/biojava/commit/0855c3de770c6bb2c6935cda9df17c3b8e045149
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Merge pull request #304 from sbliven/masterhttps://github.com/JavaMuller/biojava/commit/f069b4f0846fe8c950cad1179188f011d0c0d0cf
https://github.com/andreasprlic
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Adding some more non-deposited files tests, #305.https://github.com/JavaMuller/biojava/commit/782e2f766a08ba5479d6c1dae888859855f24cd9
https://github.com/josemduarte
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https://github.com/JavaMuller/biojava/tree/782e2f766a08ba5479d6c1dae888859855f24cd9
Reverting parser change: removing pure non-poly chains is a bad idea.https://github.com/JavaMuller/biojava/commit/bec799055097e2b940c8b7f0238214816e66a3e7
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More parsing fixes, #305https://github.com/JavaMuller/biojava/commit/6f709099edf77ec7e88d03914cd6a60785bb2804
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Merge remote-tracking branch 'upstream/master'https://github.com/JavaMuller/biojava/commit/55af36080e4e66bce2ba1ab0ec1bf04603025a8e
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Better parsing of COMPND lines in PDB files, #305https://github.com/JavaMuller/biojava/commit/36a8feac58e8ebeb76d9a567479c8dc667782830
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Fixing tests: order of AbstractScoresCache.getScores wasn't guaranteedhttps://github.com/JavaMuller/biojava/commit/b99e061fffaf0cedf9325ffb6f6510632d428875
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Fix bug with flexible MultipleAlignmentshttps://github.com/JavaMuller/biojava/commit/c9ba6d19c39304f28462075019165e49cbf43d61
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lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
c9ba6d1https://github.com/JavaMuller/biojava/commit/c9ba6d19c39304f28462075019165e49cbf43d61
https://github.com/JavaMuller/biojava/tree/c9ba6d19c39304f28462075019165e49cbf43d61
Rename and move Tests for consistencyhttps://github.com/JavaMuller/biojava/commit/d8c5d2fe6025a432a240a9154b422b13bda64a42
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
d8c5d2fhttps://github.com/JavaMuller/biojava/commit/d8c5d2fe6025a432a240a9154b422b13bda64a42
https://github.com/JavaMuller/biojava/tree/d8c5d2fe6025a432a240a9154b422b13bda64a42
Merge branch 'master' of https://github.com/biojava/biojava.githttps://github.com/JavaMuller/biojava/commit/ee387202386eec3a231724a5b5c6a34686f54350
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
ee38720https://github.com/JavaMuller/biojava/commit/ee387202386eec3a231724a5b5c6a34686f54350
https://github.com/JavaMuller/biojava/tree/ee387202386eec3a231724a5b5c6a34686f54350
Remove the 3D transformations in MultipleAlignmenthttps://github.com/JavaMuller/biojava/commit/e18e02cb442c88ac3e61df9441e6ffc00aae034c
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
e18e02chttps://github.com/JavaMuller/biojava/commit/e18e02cb442c88ac3e61df9441e6ffc00aae034c
https://github.com/JavaMuller/biojava/tree/e18e02cb442c88ac3e61df9441e6ffc00aae034c
Updating SCOPe to version 2.05https://github.com/JavaMuller/biojava/commit/f78e95991247c98288ed330e42e111ffc910882b
https://github.com/sbliven
sblivenhttps://github.com/JavaMuller/biojava/commits?author=sbliven
f78e959https://github.com/JavaMuller/biojava/commit/f78e95991247c98288ed330e42e111ffc910882b
https://github.com/JavaMuller/biojava/tree/f78e95991247c98288ed330e42e111ffc910882b
Factor out Subunits definition in quaternary symmetryhttps://github.com/JavaMuller/biojava/commit/8094a8eb5553d8a26eb45ef666301c2cc779b61e
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
8094a8ehttps://github.com/JavaMuller/biojava/commit/8094a8eb5553d8a26eb45ef666301c2cc779b61e
https://github.com/JavaMuller/biojava/tree/8094a8eb5553d8a26eb45ef666301c2cc779b61e
Adding sortBlocks methodhttps://github.com/JavaMuller/biojava/commit/ecff44042a428dbdb49de3abb2c355e7c3db069f
https://github.com/sbliven
sblivenhttps://github.com/JavaMuller/biojava/commits?author=sbliven
ecff440https://github.com/JavaMuller/biojava/commit/ecff44042a428dbdb49de3abb2c355e7c3db069f
https://github.com/JavaMuller/biojava/tree/ecff44042a428dbdb49de3abb2c355e7c3db069f
Calc.transform() documentation and testinghttps://github.com/JavaMuller/biojava/commit/fdb5cb0a2deaf9f6e30dd9222591a59c068b9fdf
https://github.com/lafita
lafitahttps://github.com/JavaMuller/biojava/commits?author=lafita
fdb5cb0https://github.com/JavaMuller/biojava/commit/fdb5cb0a2deaf9f6e30dd9222591a59c068b9fdf
https://github.com/JavaMuller/biojava/tree/fdb5cb0a2deaf9f6e30dd9222591a59c068b9fdf
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