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onbiojava-7.2.4

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Commits on Jan 7, 2025

• Javadoc fix: errors in modfinder module

  josemduarte

  committed
  bb07329

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Commits on Apr 18, 2024

• Fix sonar issue S2293 Replace the type specification in this constructor call with the diamond operator ('<>')

  jlerbsc

  committed
  b182121

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Commits on Feb 26, 2024

• fix: issue #1081 Sonar S1132 Strings literals should be placed on the left side when checking for equality

  jlerbsc

  committed
  ac75f31

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Commits on Jun 30, 2023

• Try-with from sonar

  josemduarte

  committed
  1678958

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Commits on Nov 18, 2022

• vuln-fix: Temporary File Information Disclosure

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  JLLeitschuh

  and

  TeamModerne

  committed
  e3ecec5

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Commits on Nov 7, 2021

• Minor Miscellaneous formatting and import

  aalhossary

  committed
  419d5f0

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Commits on Jan 20, 2021

• compiling

  sbittrich

  committed
  1b164a9

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Commits on Jun 13, 2020

• refactor code to java 8 streams api

  balaji-s

  committed
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Commits on Jan 3, 2019

• Automatically convert spaces to tabs

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  sbliven

  committed
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Commits on Mar 12, 2018

• Removing deprecations from v4

  josemduarte

  committed
  9dbf83c

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Commits on Sep 8, 2017

• Fixing phosphosite urls and changing default url timeout to 30s

  josemduarte

  committed
  67ca7f2

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Commits on Nov 30, 2016

• moving to Java 7

  andreasprlic

  committed
  4ee39f8

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• now also accepting old header line

  andreasprlic

  committed
  8210484

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Commits on Nov 29, 2016

• fix for #610

  andreasprlic

  committed
  6f28672

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Commits on Aug 8, 2016

• new utility classes to detect if a Group is polymeric, an amino acid, or a nucleotide group.

  andreasprlic

  committed
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Commits on Jun 15, 2016

• some formatting improvements.

  andreasprlic

  committed
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Commits on Jun 14, 2016

• Added list of chromophores to ptm_list.xml file, updated unit tests

  pwrose

  committed
  417e2da

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Commits on Jun 10, 2016

• Merge pull request #502 from andreasprlic/master

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  josemduarte

  authored
  3509775

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• update for 2VH3 TY2

  andreasprlic

  committed
  58c6743

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• updating legacy chemical component and atom names to current naming conventions.

  andreasprlic

  committed
  913d1ef

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• distance have to be looked up by element name, not atom name

  andreasprlic

  committed
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Commits on Jun 9, 2016

• Adds a new definitions file so the code can correctly detect Metal bonds. Slightly more efficient representation of standard amino acids.

  andreasprlic

  committed
  b39840a

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Commits on Jun 5, 2016

• squid:S2131 - Primitives should not be boxed just for String conversion

  

  Mohamed Ezzat

  committed
  fa52fd8

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Commits on Jun 1, 2016

• Allowing detection of PTMs that interact with Terbium, as reported by @epeisach . Also less verbose PTM junit test.

  andreasprlic

  committed
  c561c3a

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Commits on May 17, 2016

• Updating change log in PTM definitions file to reflect most recent changes.

  andreasprlic

  committed
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Commits on May 12, 2016

• Merge pull request #479 from josemduarte/asymChainIds

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  andreasprlic

  committed
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Commits on May 11, 2016

• Fixed modfinder tests

  josemduarte

  committed
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Commits on May 10, 2016

• Added definition for PLP (pyridoxin-5'-phosphate) protein modification to xml file and added unit test.

  pwrose

  committed
  e814b32

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Commits on May 4, 2016

• Fix the compile errors - mainly by changin "setChainId" "setChainName"

  abradle

  committed
  a4f8795

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Commits on Mar 9, 2016

• More whitespace fixes

  sbliven

  committed
  af59f90

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• Converting initial spaces to tabs.

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  sbliven

  committed
  2417c23

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• Remove trailing whitespace globally from .java files

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  sbliven

  committed
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Commits on Oct 6, 2015

• Converting all line endings to Unix.

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  sbliven

  committed
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Commits on Jan 30, 2015

• more updates of wrong resource paths

  andreasprlic

  committed
  f21dec3

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• Refactoring of all package names according to #245 #242 #240

  andreasprlic

  committed
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