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Title: History for biojava-structure/src - 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-structure/src - 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-structure/src - biojava/biojava

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Adding safeguard, bug introduced in #1116 and reported in Biojava-lhttps://github.com/biojava/biojava/commit/7c3909fcff05b76440632518d6350474ca4365da
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Bugfix: edge-case with no equiv residues in alignment wasn't dealt with and led to IllegalArgumentException.https://github.com/biojava/biojava/commit/423cd86fbc2355f9943a3bbd81597c3d0c231627
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Fix #1079: Use isEmpty() instead of size() == 0https://github.com/biojava/biojava/commit/3f039fd3f5128e3f97981873f9855f45949848a0
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Fix RSPEC-1940 boolean checkshttps://github.com/biojava/biojava/commit/0af196ffd522f98aa093dd569659438f1ab81ebf
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Update biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.javahttps://github.com/biojava/biojava/commit/aa0d5767badb81bc672127343ae8a1ce3ea84ad9
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Make entity type case insensitive. Also improved docshttps://github.com/biojava/biojava/commit/501a09e2590965318d0a85c52d1759291060f450
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Update biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.javahttps://github.com/biojava/biojava/commit/48cb462e137a17d5161f390bbf265a11bc4f48ee
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Revert "Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_ref"https://github.com/biojava/biojava/commit/fdf98644c046416531cb53da0f67e8b7fc6a44cf
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Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_refhttps://github.com/biojava/biojava/commit/8286260589643583c6d631a989b708b4d8c7b956
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Deal with some missing fields in IHMhttps://github.com/biojava/biojava/commit/a6723d42a22166de949bed6a6c4f4f1f29a87ee7
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Merge pull request #1106 from josemduarte/cifparsing-lenienthttps://github.com/biojava/biojava/commit/77c2911e50938d8bca9c236aa328982f96004112
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a5b46abhttps://github.com/biojava/biojava/commit/a5b46ab0bb748317516dbdb95f18bb8ab30fb2ca
https://github.com/biojava/biojava/blob/a5b46ab0bb748317516dbdb95f18bb8ab30fb2ca/biojava-structure/src
https://github.com/biojava/biojava/tree/a5b46ab0bb748317516dbdb95f18bb8ab30fb2ca
Fix: first model is model index 0https://github.com/biojava/biojava/commit/324319e20d5c2ffcbe8b2d10189e369b590a34aa
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
324319ehttps://github.com/biojava/biojava/commit/324319e20d5c2ffcbe8b2d10189e369b590a34aa
https://github.com/biojava/biojava/blob/324319e20d5c2ffcbe8b2d10189e369b590a34aa/biojava-structure/src
https://github.com/biojava/biojava/tree/324319e20d5c2ffcbe8b2d10189e369b590a34aa
Bugfix: ASA calculation was by default using all models. Now it will use model 1 by default. Added new constructor to choose model.https://github.com/biojava/biojava/commit/c45c3dd05beaed3f214b991526f713d9090b5e1f
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
c45c3ddhttps://github.com/biojava/biojava/commit/c45c3dd05beaed3f214b991526f713d9090b5e1f
https://github.com/biojava/biojava/blob/c45c3dd05beaed3f214b991526f713d9090b5e1f/biojava-structure/src
https://github.com/biojava/biojava/tree/c45c3dd05beaed3f214b991526f713d9090b5e1f
Another safeguard, that applies to some PDB-IHM entrieshttps://github.com/biojava/biojava/commit/12dcb2ce3c1a03d67798311ca7cf6fd26e12563f
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
12dcb2chttps://github.com/biojava/biojava/commit/12dcb2ce3c1a03d67798311ca7cf6fd26e12563f
https://github.com/biojava/biojava/blob/12dcb2ce3c1a03d67798311ca7cf6fd26e12563f/biojava-structure/src
https://github.com/biojava/biojava/tree/12dcb2ce3c1a03d67798311ca7cf6fd26e12563f
Lenient to missing atom_site.occupancyhttps://github.com/biojava/biojava/commit/65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
65d3dcdhttps://github.com/biojava/biojava/commit/65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a
https://github.com/biojava/biojava/blob/65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a/biojava-structure/src
https://github.com/biojava/biojava/tree/65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a
Handle more missing fields in struct_ref_seqhttps://github.com/biojava/biojava/commit/93c1c8f9d4c1fa3d12d2c7f7d250532ed6b62098
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
93c1c8fhttps://github.com/biojava/biojava/commit/93c1c8f9d4c1fa3d12d2c7f7d250532ed6b62098
https://github.com/biojava/biojava/blob/93c1c8f9d4c1fa3d12d2c7f7d250532ed6b62098/biojava-structure/src
https://github.com/biojava/biojava/tree/93c1c8f9d4c1fa3d12d2c7f7d250532ed6b62098
Merge pull request #1103 from josemduarte/cifparser-gemmifilehttps://github.com/biojava/biojava/commit/f880d18fcb7655adaff2845491e99d1ed8953b51
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
f880d18https://github.com/biojava/biojava/commit/f880d18fcb7655adaff2845491e99d1ed8953b51
https://github.com/biojava/biojava/blob/f880d18fcb7655adaff2845491e99d1ed8953b51/biojava-structure/src
https://github.com/biojava/biojava/tree/f880d18fcb7655adaff2845491e99d1ed8953b51
Javadoc fix: remaining errors in structure module. Mostly obsolete referenceshttps://github.com/biojava/biojava/commit/2bbc82438cc8aba6dbbfbc362aef4959a0714918
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
2bbc824https://github.com/biojava/biojava/commit/2bbc82438cc8aba6dbbfbc362aef4959a0714918
https://github.com/biojava/biojava/blob/2bbc82438cc8aba6dbbfbc362aef4959a0714918/biojava-structure/src
https://github.com/biojava/biojava/tree/2bbc82438cc8aba6dbbfbc362aef4959a0714918
Javadoc fix: most other errors in structure modulehttps://github.com/biojava/biojava/commit/0c7e9f5fc52f79e942cf1780baafde473b459368
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
0c7e9f5https://github.com/biojava/biojava/commit/0c7e9f5fc52f79e942cf1780baafde473b459368
https://github.com/biojava/biojava/blob/0c7e9f5fc52f79e942cf1780baafde473b459368/biojava-structure/src
https://github.com/biojava/biojava/tree/0c7e9f5fc52f79e942cf1780baafde473b459368
Javadoc fix: many errors in struct align packagehttps://github.com/biojava/biojava/commit/435ebe98b58bf9cc044dc37414e4ae75a08835b1
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
435ebe9https://github.com/biojava/biojava/commit/435ebe98b58bf9cc044dc37414e4ae75a08835b1
https://github.com/biojava/biojava/blob/435ebe98b58bf9cc044dc37414e4ae75a08835b1/biojava-structure/src
https://github.com/biojava/biojava/tree/435ebe98b58bf9cc044dc37414e4ae75a08835b1
Javadoc fix: many errors in struct align packagehttps://github.com/biojava/biojava/commit/d2053f30741f1361ab5cf377f8e0da240a7ba59f
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
d2053f3https://github.com/biojava/biojava/commit/d2053f30741f1361ab5cf377f8e0da240a7ba59f
https://github.com/biojava/biojava/blob/d2053f30741f1361ab5cf377f8e0da240a7ba59f/biojava-structure/src
https://github.com/biojava/biojava/tree/d2053f30741f1361ab5cf377f8e0da240a7ba59f
Javadoc fix: many errors in struct align packagehttps://github.com/biojava/biojava/commit/2b33a56bd2fa555c62197ad8f81fff1f46722731
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
2b33a56https://github.com/biojava/biojava/commit/2b33a56bd2fa555c62197ad8f81fff1f46722731
https://github.com/biojava/biojava/blob/2b33a56bd2fa555c62197ad8f81fff1f46722731/biojava-structure/src
https://github.com/biojava/biojava/tree/2b33a56bd2fa555c62197ad8f81fff1f46722731
More lenient parsing if some fields are missing (e.g. in files output by Gemmi)https://github.com/biojava/biojava/commit/5a5052428c88669d7bb31a92dcd2718c3cbb9788
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
5a50524https://github.com/biojava/biojava/commit/5a5052428c88669d7bb31a92dcd2718c3cbb9788
https://github.com/biojava/biojava/blob/5a5052428c88669d7bb31a92dcd2718c3cbb9788/biojava-structure/src
https://github.com/biojava/biojava/tree/5a5052428c88669d7bb31a92dcd2718c3cbb9788
Javadoc fix: some more errors from structure modulehttps://github.com/biojava/biojava/commit/52d10538768889d97e23e5fe245434c956723091
https://github.com/josemduarte
josemduartehttps://github.com/biojava/biojava/commits?author=josemduarte
52d1053https://github.com/biojava/biojava/commit/52d10538768889d97e23e5fe245434c956723091
https://github.com/biojava/biojava/blob/52d10538768889d97e23e5fe245434c956723091/biojava-structure/src
https://github.com/biojava/biojava/tree/52d10538768889d97e23e5fe245434c956723091
Nexthttps://github.com/biojava/biojava/commits/biojava-7.2.5/biojava-structure/src?after=5d047ab428b176a437131d31171c7f779caa239e+34
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