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Title: Commits · VividcodeIO/biojava · GitHub

Open Graph Title: Commits · VividcodeIO/biojava

X Title: Commits · VividcodeIO/biojava

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

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

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

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

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og:image:alt:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. - Commits · VividcodeIO/biojava
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Merging from master to biojava-ffx integration branch.https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/3fc00bef825002bbd835a175dba4328d840fd309
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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://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/8fe919aa6f201793c41780a09b4f7b9c3d1f600d
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Merge remote-tracking branch 'upstream/master'https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/df98f2ef4b69f977000400fcd011761afb1d0491
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Merge pull request #311 from lafita/cesymmhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/bd62ae259019ae9589b08d05557eaa5cf1d179fc
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Merge pull request #312 from lafita/fix309https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/63861777e66ae5abd5407f194fa41e408d789282
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Use C-alpha Atoms in AltLocs Testhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/f2c25d57de9597b290d336523333aa8dba938810
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Fix StructureToolsTest to pass according to changeshttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/2927b321308cc20008a4e8aa451359806cd1683e
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Allow non-refined result, only self-alignmenthttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/6beb84973b8037383639b59393f95a9e30174071
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Fix demo issueshttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/90b44036d0c503d81478190f4fc836e8c5037d1c
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Crate Test for consistency in getting representative Atomshttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/edb9e7312263716e58fdb6385243407504c2da8f
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Make getRepresentative Atoms consistenthttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/b1bd53489399431df8f93df548fd31f6afda3580
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Fixing issue in getAlignedResIndex, now the mapping will work forhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/7f1a7f3cb8cffd6ac710dbea36f032e8cbc45f51
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Add Demo for CeSymmhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/e5cfa6b7ce4cc2fc30ea5f14899549c09fa77a7d
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Port CeSymm for internal symmetry detection code to BioJavahttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/05c6c35753d305d0d828db73ffa56406a400a71f
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fix for #306 - now checks provided URL if it contains the string ".cif" and switches to mmCif parsing accordingly.https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/f9d0480604d5c6efa668de04d76ab19078ac10c4
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#308 adding a test that demonstrates that fetching mmCIF files from remote URLs is broken. Also tests for correct parsing of compressed files.https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/66cfcdcc2e013e4c9d279656bb59dc04ea9afffe
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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://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/ffdc278c251092da01dca94f1891ab7c95753a6a
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Some cosmeticshttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/2a16a64ac7a33ea6f1ff0e97b124a4485acfeff3
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Making tests less verbosehttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/0855c3de770c6bb2c6935cda9df17c3b8e045149
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Merge pull request #304 from sbliven/masterhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/f069b4f0846fe8c950cad1179188f011d0c0d0cf
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Adding some more non-deposited files tests, #305.https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/782e2f766a08ba5479d6c1dae888859855f24cd9
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Reverting parser change: removing pure non-poly chains is a bad idea.https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/bec799055097e2b940c8b7f0238214816e66a3e7
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More parsing fixes, #305https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/6f709099edf77ec7e88d03914cd6a60785bb2804
https://patch-diff.githubusercontent.com/josemduarte
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/6f709099edf77ec7e88d03914cd6a60785bb2804
Merge remote-tracking branch 'upstream/master'https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/55af36080e4e66bce2ba1ab0ec1bf04603025a8e
https://patch-diff.githubusercontent.com/josemduarte
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/55af36080e4e66bce2ba1ab0ec1bf04603025a8e
Better parsing of COMPND lines in PDB files, #305https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/36a8feac58e8ebeb76d9a567479c8dc667782830
https://patch-diff.githubusercontent.com/josemduarte
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36a8feahttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/36a8feac58e8ebeb76d9a567479c8dc667782830
https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/36a8feac58e8ebeb76d9a567479c8dc667782830
Fixing tests: order of AbstractScoresCache.getScores wasn't guaranteedhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/b99e061fffaf0cedf9325ffb6f6510632d428875
https://patch-diff.githubusercontent.com/josemduarte
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b99e061https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/b99e061fffaf0cedf9325ffb6f6510632d428875
https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/b99e061fffaf0cedf9325ffb6f6510632d428875
Fix bug with flexible MultipleAlignmentshttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/c9ba6d19c39304f28462075019165e49cbf43d61
https://patch-diff.githubusercontent.com/lafita
lafitahttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commits?author=lafita
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/c9ba6d19c39304f28462075019165e49cbf43d61
Rename and move Tests for consistencyhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/d8c5d2fe6025a432a240a9154b422b13bda64a42
https://patch-diff.githubusercontent.com/lafita
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/d8c5d2fe6025a432a240a9154b422b13bda64a42
Merge branch 'master' of https://github.com/biojava/biojava.githttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/ee387202386eec3a231724a5b5c6a34686f54350
https://patch-diff.githubusercontent.com/lafita
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ee38720https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/ee387202386eec3a231724a5b5c6a34686f54350
https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/ee387202386eec3a231724a5b5c6a34686f54350
Remove the 3D transformations in MultipleAlignmenthttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/e18e02cb442c88ac3e61df9441e6ffc00aae034c
https://patch-diff.githubusercontent.com/lafita
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e18e02chttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/e18e02cb442c88ac3e61df9441e6ffc00aae034c
https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/e18e02cb442c88ac3e61df9441e6ffc00aae034c
Updating SCOPe to version 2.05https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/f78e95991247c98288ed330e42e111ffc910882b
https://patch-diff.githubusercontent.com/sbliven
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f78e959https://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/f78e95991247c98288ed330e42e111ffc910882b
https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/f78e95991247c98288ed330e42e111ffc910882b
Factor out Subunits definition in quaternary symmetryhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/8094a8eb5553d8a26eb45ef666301c2cc779b61e
https://patch-diff.githubusercontent.com/lafita
lafitahttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commits?author=lafita
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/8094a8eb5553d8a26eb45ef666301c2cc779b61e
Adding sortBlocks methodhttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/ecff44042a428dbdb49de3abb2c355e7c3db069f
https://patch-diff.githubusercontent.com/sbliven
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https://patch-diff.githubusercontent.com/VividcodeIO/biojava/tree/ecff44042a428dbdb49de3abb2c355e7c3db069f
Calc.transform() documentation and testinghttps://patch-diff.githubusercontent.com/VividcodeIO/biojava/commit/fdb5cb0a2deaf9f6e30dd9222591a59c068b9fdf
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