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Title: Javadoc errors cleanup by josemduarte · Pull Request #1104 · biojava/biojava · GitHub

Open Graph Title: Javadoc errors cleanup by josemduarte · Pull Request #1104 · biojava/biojava

X Title: Javadoc errors cleanup by josemduarte · Pull Request #1104 · biojava/biojava

Description: FYI, I'll merge it. I'll see if I can introduce javadoc linting in CI to avoid any new errors coming in.

Open Graph Description: FYI, I'll merge it. I'll see if I can introduce javadoc linting in CI to avoid any new errors coming in.

X Description: FYI, I'll merge it. I'll see if I can introduce javadoc linting in CI to avoid any new errors coming in.

Opengraph URL: https://github.com/biojava/biojava/pull/1104

X: @github

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27a88ff Javadoc fix:

josemduarte Jan 3, 2025

https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/27a88ff9780f0c67561b046ad44540f779ff4c02
193287b Javadoc fix: param fixes josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/193287b7bff37997d72da9ab188261667f1b1f21
d104809 Javadoc fix: html-like tag not allowed josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/d10480957234d8591f79381f962a985aec1a2c74
2fab7b0 Javadoc fix: html escaping josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/2fab7b03503a48faff1dde8a86254e1b287dd063
1c8d587 Javadoc fix: bad tags josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/1c8d58788845e1418b83683734eef997951734c5
13e3afe Javadoc fix: all other errors in core module josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/13e3afef7566de8d5662eac8438c3dfa9edefa42
71fe179 Javadoc fix: all error in alignment module josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/71fe179011fbd17a04876da57a4e4f49f0845338
ed7ab8e Javadoc fix: a few errors from structure module josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/ed7ab8e32d958730568898f733fccd0f0d42273d
280f239 Javadoc fix: some more errors from structure module josemduarte Jan 3, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/280f2398e7e287c8e3c41d3e09750fb9e0d285d8
52d1053 Javadoc fix: some more errors from structure module josemduarte Jan 4, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/52d10538768889d97e23e5fe245434c956723091
2b33a56 Javadoc fix: many errors in struct align package josemduarte Jan 6, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/2b33a56bd2fa555c62197ad8f81fff1f46722731
d2053f3 Javadoc fix: many errors in struct align package josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/d2053f30741f1361ab5cf377f8e0da240a7ba59f
435ebe9 Javadoc fix: many errors in struct align package josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/435ebe98b58bf9cc044dc37414e4ae75a08835b1
0c7e9f5 Javadoc fix: most other errors in structure module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/0c7e9f5fc52f79e942cf1780baafde473b459368
2bbc824 Javadoc fix: remaining errors in structure module. Mostly obsolete re… josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/2bbc82438cc8aba6dbbfbc362aef4959a0714918
aefa34a Javadoc fix: errors in structure-gui module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/aefa34a52f1c208e3b43d005d5db336052cef900
3580f7b Javadoc fix: errors in genome module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/3580f7bac804f3305411a7a9d41bdb47cb836b4e
bb07329 Javadoc fix: errors in modfinder module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/bb073294543ce4c4096d0389ab89aad9d33675f2
d483bba Javadoc fix: errors in ws module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/d483bba04798f62fec44f6a83262a1c74370202e
0183dc6 Javadoc fix: errors in protein-disorder module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/0183dc629b76a2632dfdf271462a3a90fbef085b
24310c3 Javadoc fix: errors in aaprops and survival and modules josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/24310c315b565389cae7c4d38f00908c2bedaee7
b55dc80 Javadoc fix: errors in ontology module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/b55dc80cfba061dcc9e4ca09bdc4f6c5c9137037
c3079ea Javadoc fix: errors in integration-test module josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/c3079eaed9fb58e89a8a286f62e919cfbf6dc7de
48c29b1 Merge branch 'master' into javadocfixes josemduarte Jan 7, 2025 https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/commits/48c29b1c3b8ef3020f147beb1d45240d269b33c1
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SequencePair.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-af42073752e7dccb013091357e5bb0ad6822bc9dc7289ccd83bdf1fb04a5e6f4
SubstitutionMatrix.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8b94130cda13d3d76ea0fd3557060435e17ec7fe889d6e33c69877a5b72fb1d3
ParserException.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-faf043a4ef15e3685b839c6fee555ccfd172136f70673f9e3bcd70fc9b487b68
Hsp.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5e153f287c7f5631feb1a90bfc3f69135345dc26a4b51224f493379a057a3779
ResultFactory.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ecbeac5bd401b793233e3de90941885dddc80fbbb24db657158de500595e0d5a
SearchIO.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e2c4b52e77455bebccd63b1685f71b39ba7c6e0f94e03a79908858729d718bac
BlastXMLParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f3d22787ed9dc78dffe145d9975c38ef80fe48e04c4d1b3dafbddfd674e2b460
CDSComparator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-02933405dcd41d9382577ee04f025c304d274ab404824b92f6e6c81efbc00846
CDSSequence.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-009a077f4fe21665ea29bc73eeffe4b54b935043de771d114cd676b9ed438f7e
DataSource.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-689f48e5153b4428d21bef4be091b59cfddd5d594f8e9c8887b59ff6227e1874
ExonComparator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5ca05e1b543a3b6a3eaf8732e5ef4d7af6ab91a14babd05e846a53e814abde9c
RNASequence.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3bb20d49a7963f1324b5ddfe752cadb71aa124bb5d32fceda91045be11ec52f9
SequenceComparator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-4d9a904c7dd4a058ee08186b18a2cfdee78876972daa88b637bfbf8023b32d7e
Edit.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-52236e19cfe0f8534131c1f9500e00c4dcb1b7db35c2e765d34d3fbd9bf57fa3
AbstractFeature.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0992de11961fdf916d945b59473d427764e2f93c743adfee35b52661bac8b7f6
DBReferenceInfo.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-7cb863a29f032b617fde2cdd02f91b01c34c08b05e98a6cfac34e3a45991e04e
DatabaseReferenceInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9019f919dbdb0870faa03ce13ed8e01312ef95392b1206a862ce5ab7a7b5563a
FeatureDbReferenceInfo.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-facc85764393a612cac5ae2c1225355ebde0f95c57597dfbc248fb3f838303de
FeatureInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-4811d1cbe601714120562e32ebf2ee164bf063bc1c628e4037745726886a7abf
FeaturesKeyWordInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8943c7778f510179ac778cc5dd0d8d9158cedfa0cae73db228b2c719ddc4093c
QuantityFeature.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c810753870fe20bd98d79f905e48fb9f63d7dbeefb117760c402b8c65e039fe1
TextFeature.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-bbe1eb92c3254ebfdb5a83cce29cc7735055fffe967155a232ace688420986ed
ABITrace.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6c71f5d7312bed6df5ac60971e26e80508c0b607a05e06f93dab1d65ea93556a
BufferedReaderBytesRead.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b855c06415041448b5d1d235e515b5474e0c8da57808eed4813346120400de54
CasePreservingProteinSequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f5095102320326bb5560676a014760c745959e113de7f4a882881ee7719d20d7
DNASequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-823d2b3954bf5b023a2fd9a617ff0054d071bb7b84359f0be4ef63b56d2411ae
FastaGeneWriter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9a6e7dc4461a242cbe707b4834e460bcf723453a0e53d7c325b1b677d82f66e0
FastaReaderHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-4bcbb8088686c628b07960e8dec3738dd10f56842ea45737717e6c5740723ebc
FastaSequenceParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-92558d6b29d7cfb233b6b47e604f19ac28e8721094908c54a295e71893f8a043
FastaWriter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8e49435fc4903b028415c24e53bf5efe03a747415b062baf6d53bcac83193a9d
FastaWriterHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ccd945e27d9d29e10cd585a9c56e7196e46a43c65423b614610bb5e92ac20f39
FileProxyDNASequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-76b0f0f6580174a060ce9bc678946ddc41de29bb6d903964c3f654006bec8142
FileProxyProteinSequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6f91f2db73739311ef9a1f2070816ca87dde9933263b5c103e8fc5f680acbaa6
FileProxyRNASequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-16cb8c765bb680efa8a6d93a32780468f78eda892a12ff114a272c295143ed1e
GenbankReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a7b326d8bdd6c3945b25f1b4a673152ef6bd04ce5c9c51c242e20d2bd546e67f
GenbankReaderHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a54bb17b3bcdc82352e1758c045822567f091ae7ab68aafe70f97987a0121174
GenbankSequenceParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d0e1c01d087d1ef30aa0849d17646efb8624d07ac654b19e9f6e72a46ccb4407
GenbankWriter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-eaf377ac924f5e7093b55f9f10599d75a7957cadd7e4dd96a8a13570ec542bc6
GenericFastaHeaderFormat.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a4906f3193438710c0b8b5fa659177d93da7663a13bad0fda31953c945f25312
GenericFastaHeaderParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5f2c668bbfa2f76899e5a430892b10a921062d7f12896c498a64f5763324cf39
GenericGenbankHeaderParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-32ce37b4d3b320f8c4411dde9bc04c3104c7f0a971367955dc85e0b7a8c7066c
IUPACParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0fbe82602493339e48b690fa777f666202d7ba8b13871dcd61f5081b08da58b6
ProteinSequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ea4a6ad27b1da8018760903c134fd82c7901d93e3f233e3e3a4243f90b9efed9
RNASequenceCreator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a123381c7896adb2b06ce517aaafb4c8256dcb98ccdda49497fe90c0e2a5c38d
EmblRecord.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-82be4291e0454c8d1eb0dcbbf5617c05b623ea41ad5b2623a3a090a8e8e601cb
FastaHeaderFormatInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e2438913e45f9c702f0780767178a55e1fb36e21e05d80ee9825a3ee2a9540cf
GenbankHeaderFormatInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c5952dba7543007703a807d72cdf2372eff5a3d2a040fd6dcd4f7660a017f89f
SequenceCreatorInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ae332343c0d54fcdcd294bf7ae9ba508f550edebc99e052dbb016136b9d70995
SequenceHeaderParserInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3d62669b3092202e5607ab7649117b9e83074a2294ee2e97eec520f65411017f
SequenceParserInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c67c5461ef86aaff6b6d3cf25d5f07663a71138b684917bc4ab62450d5070e16
IOUtils.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-41377fb3419efbf87f02bdf83e275529351e0c337d6e235a441ee54aeca84ae9
GenbankProxySequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ff53f07fa98683a6b939a851aba8156ec5dd62e7d9e090fdee21047da8db713a
SequenceFileProxyLoader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-041374f3ca8cb1eacfe9ad9ffd80136dd1267be6dc2f6e54603318aaf14be0d8
StringProxySequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5b75ba76e53bc75e51b41b07611e2bd88507beaf7a407e86d5c26c71ed78493c
UniprotProxySequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-44a81c15f84c3804e70de3a9b45fe5425cc0455857be11926b2efdf075dfdca9
LocationHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-669ea49b8855517ca1fe96eecec91849edc0afbb79d3706b95aebcf0f4ff56b9
SequenceLocation.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-fe480ce48eafee3adaa2036d85a5e24ed6afe9bc90e649e49e4391b523a62a77
Location.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-03eeabe84c5304f0c90cf133d7036c00038c583f2aca74d52b2d5ad5f5d103e1
AbstractReference.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2b743a3627cf95670892350584d6a3cb7a782037ec734216819b0d5a0b428af0
GenbankReference.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1e67614cbb92d0421da1803dde2a03e9406153fbdd3fada130866ca2d129787e
ReferenceInterface.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9968f93823f2e4c8fca217a3de451390a08829ecaf30ca4eb819fca6c9361ccc
ArrayListSequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5796003952c9c544c9624486b86d2011645351684ec973f687b553e0a01680e9
BitSequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-358ce018ffa666f9f714e36cb144f494da33b5211c14a5890d51aeca4f8f734d
JoiningSequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2318096a039c33d4ba057e0f206258f1c136a899bdc937719cb12ec84b1a222a
SequenceAsStringHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1be25d5d7ca2b71bcfe13df9836b86ab341830f15625d0644e4641c7c68a6c09
SingleCompoundSequenceReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-dccc6bc4066b9a47bbb93caffeea6ca4cf69898f78a28e99d0bbffc739fe3a10
AbstractSequence.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-903dc8e283c52c20981a6b4060e4e2bfb68504321e312ad300ba0fcebeb7fbb1
Compound.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1499970adc10206f9ccd53fa9580f8c165b1c0c94c9fd8d0ba1bab6bebecbd18
LightweightProfile.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1b4f3941aed234286e33f99a716007b54276dc3e8a912caf8a8e0cd912fa03fb
SequenceMixin.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6ab0096b3bb89de49030f1523c40f742957acac9239f63dc4f981639b2e134c3
Table.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8afa9d10b8dfca13101faf65d93bbf74755d219d4be834fe181ebaa88cd04cc5
TranscriptionEngine.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-295750f10e2ab59cc921901805917e101358d75df331261bcd052eeb2c8f15ad
FileDownloadUtils.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2b74ace57825d99fe8102b083c13d081dde9fc3493487afba789dea427a798b6
FlatFileCache.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-63c410e102e73ccb27f6ba9a0a4be7904aedb3c0b04366e77069c8f24c223f1d
SoftHashMap.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3938c31cce7fd8b9ffe5ba35c4e907db35f6c0bb2f8e769bcf255d0c8f8e0321
StringManipulationHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c3f55925b86ec084bf0dc07c052b94b635f40e680cc7eb5fd08f8b66e6c518ae
XMLHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-80508f63e1f876ca985e1d04aa7b4f8259332bce4b67d6d91e6aac83c5085379
XMLWriter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b414a5afc3e3032b0aaa7aaf1efe592cd6093c22d292eae90500472ac120a51f
FastaReaderTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e3b389701567c456207f754ad20f1a880cd95bcd4d40119d7253eb010069ae0a
GenbankCookbookTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6505f132f69b01d9c31c823cf7cb8b173a3cbcc44f007b63dbbf9cadd687a566
GenbankReaderTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0c3832ae8c611fbc2130517f881796ea7380fe4bef0c46fd5fd16c0631068ab9
GenericFastaHeaderParserTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b51e99e868caa91f994ac2b8ae7cced843aec68dd375e5117762b92348ffdb63
SimpleGenbankProxySequenceReaderTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-4942b714e06b1515cda12ce204278a9a5db545beae1129285712f68c6e44860c
GeneFeatureHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-94e39f954411e05eaa9edc35098098ad2ccdad026a438559cfd32565c10ff47b
BlastHomologyHits.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2a958953be3268b598a9ca214abc87e15a02fbcf1cf8605b3503ec9aee8a16d6
GFF3FromUniprotBlastHits.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3122e7e000fd35688e72f9fee3bf05c7d36a032543bd9d00c60270207c1dc842
GeneIDXMLReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d64735cad944b5caab52e2d47b170a20f0171a1fe4c8ce39ab55c046119c80c6
FeatureHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-75d855dd01d55988155b158d81a5dc32c5a250295c53d7fd5318d1a0c9ca95fc
GCStats.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-eb702228ade25db339ead24bbd83972db1c967d2c5e112e6efbcbf97515dcf2c
GFF3Writer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2ca1eb25b0dc3dcec1284c32409986a800746305fb175666dbfc014ae12b53ff
Location.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-76153d2d2ab3a6f23071d152919d534566d27e5a701ea681a3bef62e4eaf1e72
BlastXMLQuery.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b37d5675a90fc5cc079c3f2ba474b29122a160d231c51234d0bca0bbc9e7cc2e
OutputHitsGFF.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f2a00d49c29061022a132d3213c4088c6d8a9def2a7b564d517cb0ad678b76af
SplitFasta.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6cea4babed861ba77dac92889062b0aa7237e3af3a6f66084c10ab1873b6a3a9
GeneFeatureHelperTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2d6e8cfef9c856a1fbeb82f7c74bc2dafa54660fdbb8d1347abc8ee5afed97e4
ScopDescriptionTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c2bb0109f5a318149bdedc85661d1c8f1ede3f946ecbdf862c0d05485ac39db9
StringManipulationTestsHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a133d3a200482839a56769598a7a41134e1503b4c8bc2d4b8d632dade39a21a5
Component.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-4a0adb720e558511b875cfe59194269aae0fc81659a7028ff5bdfb9b26e1042d
ModificationLinkage.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2f3547f6ed01f02d26207614cf83fa3091546bd457c798976a932a1d15047277
ProteinModificationRegistry.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c1036aa8cadac4049aef7b624e2c872eee7004fa5689b7d54cf3a10d7242a3aa
ModifiedCompound.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f782b7f2acf70451da9554220f5da9b1851f3e6b174e3d1584d343a62053b81a
ModifiedCompoundImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8d16b80db0877cd4a34ba8c47c6deb97e65c4aa85c29fdf8232916521695a8c8
Ontology.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-073e21097c80e74fe56ed64a466d6ab9e657b6c0f443b81c12c58c8e834c23ff
Term.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f9891c38127ebe30589cf6031a12605f6ace3c0819615d64189dec02b13f89e3
Triple.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-94ccd03cff2cc17fa743db69293d8f8647f725cfaf8526f4164d6b32237cf359
TabDelimParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-23644e9dba60420408858c991b6a85337c5940d274ed49670571c4a5ca479027
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-314038ed9c9ad742538caf1783c97b32f0a04883ef253751af37b79973c0c64e
OboFileParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-fa792db4cc1ddc1720a614d98da9ed6dd6ffc1278edbadc6265903dba96f7390
Annotatable.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-20c14e66ea81ba745a15fe669eb11cdbee34ec286e7755e69859985c84d6c99c
Annotation.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b529ded7bbcbaf9e0394fe0092fff30155bca1049b6122af92ace418679fbff3
EmptyAnnotation.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ec7a38e01ef5b89401ef9db8ace84fe94acfc635d803b8bec788ad375fb095da
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-da75f62f6fe7db95f13a10bc5d1c26f35123b4ea6c657ed6834d8a1536a28ff9
Jronn.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-fad5f1139c447a86ace354b9757804f0bef991e17fc640a20838bac72ca4c998
AFPFromFasta.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f778591ae5fee36b62a488ef596e220a7ab8c505fc01766bbb7fcd23f9513788
AlignmentCalc.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e664d751cc0e8db1f0d2fcf374c1c027cb282cdacbd9a052cc469654aa4fe047
DotPlotPanel.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1f491056a009e6daf6cc2c9a09757b367d54d81d50a949d2a983dcf0650cdbf9
MemoryMonitor.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-38b6d48f4c152ccad9843519a1d9909bdd35c350e0718a318a234a0266fd2044
SelectPDBPanel.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f26285adba7d57f69ebcbe9b077991ba48ed1a64765efaa47932056617159996
MultipleAligPanel.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5fc8937ed1abe2f084e9f9baa920a26997b6d8b4731db5317fb707eee5cf1fea
AbstractAlignmentJmol.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b73e12606dc33ce8831aef3c0d5f7a7686ae7c5fcf43b779f36a2f7e640e581a
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-bab1386cdd1742aca5844684b4b1ab9c6bb454c82aacc53163bc23f12456b5f7
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0f8a936506bd01ae94e396a381b3e55fb6aa71d2e1c65e60f857e617741ade86
ContinuousColorMapperTransform.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a4f35b80d0753c1b0e157e00c5d94a55b37ffa6db8b16d5132fc498da1a45378
HSVColorSpace.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-54aca0e0d8952c09e30323734c28a81d77133e35571e4f30c538253fa798ba88
LinearColorInterpolator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1b1f7791ab778a1eb54ac137ea1ff2c45eb3ed803ba6b410dfccafa779037550
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ae21fb0c7f40288cd43953440b2e8e0dd842147b102d5529bc083232b575ebbf
SymmetryDisplay.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2ab35634665f5198e29853f7450678bca6664f799667a4700fc0ed3e6933efa3
JmolSymmetryScriptGenerator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3b1314cda9560c151ef901873f314c0b51f6856af39668771cda1f8a29a60fb4
DemoChangeChemCompProvider.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-800889e0de33f09cc3863863ffb460f4abf62ab065f69ba854cab90d0b1f7999
Atom.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d4894ede42a8b6c5d4aafb0f7bad48fe4745908573643540f2646dbef705c15a
BioAssemblyIdentifier.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2e22cff1557dd4c1b1f1dbd6b3ad3ac51d2913ba1f5bedeadb6352924655ebf1
Bond.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-887bfc1bcda9a380a8759c15facf30b40f1d4955478c69c01479caeb6ada0e19
BondImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-6797b62a8dcc93a564e0cbb18ed22ab9c54c40ea4313b0ed5b430b51f483f0b5
BondType.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8b85cf764689671f436899affca065acfdd4133d3bd5834c708d5362e6948e31
Calc.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d95b564188d5b484a5ad399bc3f3d9b52bc4c92bea5d6c6f139d34b2f5bea82a
Chain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f29f6389701652caccff290f6889c11ed192a52952a4e57b596aafd3c7362282
Group.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d732eaf169502e9bc35dbeab0ab43058c84d958791b95900311403f0f5e78e3b
Structure.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9f07f8e3e1961b6016e30007fdbfee809f7d39929dc59167e409d64c6d18bde2
StructureIO.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-670034b751bcd0184dfd62e1564ddf7d69b82606daaa8e2a6ea76eea5347290b
StructureIdentifier.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-55e9cc73dfe9fa954b4abbc6133c87c36161e1e41f6c1483177a75fe811db22f
StructureImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a8cb31840d71a02640e5afc8609ece64252ef9321a7c0ac0447e74ec837eb5c1
URLIdentifier.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e880c84cf8afac023a4ddc25592b90732653fbd505a73eda83ebdbed66ba417b
CeCPMain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2682a1be96cc3ba7069d224e26c7a1595feb9d55ebb9f7eb396dede86fb3325c
CeMain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-63e9d9c92a4dc11c72e648d73fd629e38da410b126e74a19499d2a51c62060e2
CeParameters.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f868606fe149f339997f77490d6460c0c02d038c4667d634e0da69d001b623cd
OptimalCECPMain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-cf851eebb6cb93d3f38fdb07ee06419f6d4a9c4d2337f8e4f6d9b92b4500ae6d
AFPChainer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-99ca9aec4ae0ff174313651ca2d949ae68ba88a6628fd9ca3b2171f791f7dd5b
AFPChain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-eb71ba5801b46752be1fda0de5b9c94b25d41dd0b0312fb8d3c23cc011019f4f
Block.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1a7c12ec258b423d8801ab7eaf9dd05ce3cc9d96bdeaaae2ef9b5a1f26cf97ad
BlockImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-12ff5369fb46b52f2e1361f3c8049913cb7e3b7a179e4c11a4d3047346a552a1
BlockSet.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-98613a557e7e36e55d495a6c52ca824aea8b3b1483db59cb2c1fad9d2dbbf0d9
BlockSetImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ef87730851bbfc2e3ab5bf5b7136059954588dd738774ea6b773a15bdc0d4200
MultipleAlignmentEnsemble.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9f0a48770cbad10c6c14e04e395b9127acbd912c3ae880464178d57f62a3693c
MultipleAlignmentEnsembleImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3f744811759b5137a45f94097054e292ea1b701addcb073ca23fdfb2c66b543b
MultipleAlignmentImpl.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-144bb0d6623f4fe3b9b0c49ee7ec13783098c794ea1f9eed26108b95e72e72f0
MultipleMcMain.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2220c97e6f7c4e89b3f0d89204171a6ec654e58c36165a9b3d6333fd68e5e636
MultipleMcOptimizer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-909f0e9e8731978644ca0e2fe2751dd517aff15ffcb43c97792057d0f63de5d1
MultipleAlignmentScorer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-eae1ee16f6a5bf4968436c005305e7de0a1e1c28f530cc9a17229b7c8d966acf
MultipleAlignmentTools.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-872f7c70ecba84c415d8cb6c67a123823e423a86984cd94c013951a96dbc3cba
MultipleAlignmentWriter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-f6cba027703297322a110326aebdc1e64dad49514a8cfd137bfca5b9d1adbc6c
AFPAlignmentDisplay.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1c106a1ec5d313f5945dfbcee11678cbfccd226dfc72ede4fa20600590bf1b2f
AlignmentTools.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-7f1f39f111b8de9d1038124b72de75237edbe8765691060c32cbc5cd4d258182
AtomCache.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-cf09d4c8774528ac2de5b710b701c7713f1f03241e8af066e0da6bf7ebdeb718
RotationAxis.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b6ca0096d355e1fc39952f7e4af2f878aeb091dae8d9a50a11574a37099a3518
UserConfiguration.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1a7a7990a4163ba807514c9ebc6e7273e736863833db2c71e53276d2f0b6bfb2
AsaCalculator.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0dd60947dd070ea5584d9e88c74ba01126aed060a98862fe6f82d17fdd4ba074
DownloadChemCompProvider.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b451e1463695b76f0df7c18702af77dd2ddcb3977cfcb12a0548090d4b1c24b0
PolymerType.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9e6b602df55dffd604395a54b0751cd76ab25f434b6119b4b27df6bc8772ad80
GridCell.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-28b50c0035583f1fc40a26c3a86649c4ca1fa3cd6a1a16df618695b1ca611a23
StructureInterfaceList.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-227394d0cbffd7f05f402f093b8ee5ba000ee0261e100eee473048925dd8b6ae
EcodInstallation.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5f48fdddca942bd4575fad066efa3de396ae6cf5520801e551014ec8ca6d44d7
CalcPoint.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0c93cd1db4f3b2d8621073df2214b0cb65073c5c87cae574344be2ec10d6f895
SuperPositionQCP.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-2b14da685f157e8310cadeb7abb1fef45b8be41c5f2769ba1ab0d0418b7cd402
BondMaker.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-3ff216b81f46cc889bb22f0994fd47c15be34ffc6588d18b6b343b47ada50f7f
FastaAFPChainConverter.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0291d046dc60fc0590e2369d5953749f5ecf9cea5ee1b0075fc30e44ceed85c6
LocalPDBDirectory.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-28e458196f4923e1f2c6c92e01eaab3c2e76e8494ef1c4deb85a314186714a3d
PDBFileReader.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0145120b226685f9e22dd3d1cfaf961d29049cf2206005212f987839ad8459a6
StructureSequenceMatcher.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c73cfdf98ede0da041e30285e77eebfcf15cee0f14f827c1e1f74be4ee2e7dbd
LUDecomposition.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-63879870db35177cca9fbdc00c6f26ce0e700e0dec43869c01f6556f2a74d21d
Matrix.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-22b348cadaed3bafe8df88eb0fb666c25a0ce2966cdd26e9cf6dcf120c49029f
SymbolTable.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-cfafebaa8d068c89329a988ab738577d0470a01be4d139f2359caa2697daa5e8
package-info.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d999aff527603461677f92851154c889afe75bfa7bff4dbda744715cc69e9334
BioAssemblyTools.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-497be8b4b1f4bbaaebb15d75d58298296f8f950c8f331a8aa237df5ed1c8a37d
BiologicalAssemblyBuilder.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-05d3e7667925afdd095da21f4d18c1c0bc7a3204d778f4be817394053bc24cd8
BridgeType.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-bf8300b4f5e5f7a9e9011a73b2344c08b3b3db34d564361f400c6e5f48f73623
SecStrucState.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-0511011de206bf170856d2944d85af041dc71ee9298faddba2ef5e1fa2806e36
Helix.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8154d13fd4ef3be8459254f85449199ff81db475988b227510ffbdea45d564ad
QuatSuperpositionScorer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-dfb23b8d498623bca80916b4e8bd864333efb3ec10aa03a0983daf50b93534f4
Rotation.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9ff4ef946651ba97cdb421dce02c703174612a355f1d7488affb1cb94693165e
RotationGroup.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-d2ca8263827bd2d7ca4478f4252f6d8506d5bd9aef1c65c7507d6a6151808051
Stoichiometry.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8de014506fdec9c42fca0dc7190f7b06b01962a80371601cd721efde5e17249c
Icosahedron.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c4307c0f18d5603a4c7a225ac4c82e4a7b6566a2eded467634e3affd3be1040b
Octahedron.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-74a52d52d3a70846e06f819b45d0b20dec73e01d52f26fe2d0d5491f397af367
Prism.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e6e116a619600f8f675177237f78dc9230c7c37c2dc0207244e305cbcb4397e9
RectangularPrism.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5d409110fcac82d07b6733d4577ac0de1e5c3d5c523994ac0ab6a57b551128bf
Tetrahedron.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-c401d373ec5702a17a7aaf2b93996a3e54091c26b1da8ecb97859e96ee73c561
AngleOrderDetectorPlus.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9438f2ba4ba6a13a63713fd3ed32b30280c2dddb8d943449473e7175f8586f4a
CeSymm.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-9c88c63c114c60dfdf2f79a5ae01e634ca68cc93d8e7bde27716d3241fb4722e
CeSymmIterative.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-14611e7ceb7ada55e6577d2a4d84e662c10b5e6418d04beb0f744be26a15f219
ResidueGroup.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e4d620e52f7de4998156dd90211dea3a1d70838a5a506d1547017f5a1be219d3
SequenceFunctionRefiner.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-16f04a95fb6d9728c472d500faa7d56a9abc9a130217e6f1b05c20f2f2dab1d5
SymmOptimizer.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-ce241b9004501004c6f42c804ad827e4999527e5a38c654fa3278426c1d89622
SymmetryTools.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-abfe30972d2c031d096b56a5ffa92ddf806f38bf5d7533bd69dd37bf863548bb
SymoplibParser.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5b4b79b5f990d207e08e1b9ac1ccb5cd21cd194c56a9a3c618943fda2eb89ee7
HetatomImplTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-5d8c3e7a9e8e88d7e2dce5162bb5a8b1784e3c6b4e3565d8b7ff20a934fc31f3
PDBStatusTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-7a50cd685ab0edde3b5cddda6737183b140b7bf6836a51ee7dd6eed8f2d817a9
ResidueNumberTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-e2d94c72726602ff70a50409eba12d7914011b377b633770b760ea4fcaa218f6
SiteTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a3e65de718929ddf16a5cabf028eb72c931080a5dd9613c982597ef6f1d97c8b
AtomCacheTest.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8444a8b6dc72bfaddf21069b22955629cc4a9881f4f68be1ac08f3dfb41d493b
CoxCC.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-cc86d61b85c9c44c28ff815d86dccc13c4a09a38ac910863d2c9254e8280b3dc
CoxCoefficient.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-647eed179e5a92bf1d831c6078e097088a62946a4372dcc01b001706ac8bb67a
CoxHelper.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-8843cf24d28781f8cf4fa02b9e9831e8883116f9dd56d1e4f0f45c534353b061
CoxInfo.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-82ef9d2c4a0407dc1877d758b2c6fc5ddf6bccac714048fcae81678e861a0d20
CoxMart.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-bc8760ab113c9d20b235278430121a4f810875221d766f5a66303690b20a838c
CoxMethod.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-a00913287fd430e3ed798e07e416b29504924d720b4ca9115e2d13395104b134
CoxR.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-24b9bfeebbe7b9708760a6adf3aad823d2e41a6166c6dc166141a0e4db84975a
CoxScore.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-cabc308cfd3e49fca4f0d500ff78a8c7a0a95d9fb1059df0602758a4f7995aa0
CoxVariables.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-b0175d7504742cfefef38f3f63930b3fdf9e3bae166b8c257d41259ed825b653
ResidualsCoxph.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-145069861254c52990b30b1891b91a13415a01bfd157fad7feada89fba51e298
RiskInfo.java https://patch-diff.githubusercontent.com/biojava/biojava/pull/1104/files#diff-1ef97cff3ad052583b262b44446a5a9a0998a18480cfa732d3a30d1c7e9d6cf6
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