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GitHub / biojava/biojava issues and pull requests

#1113 - Is Pattern Match removed in new version?

Issue - State: closed - Opened by tlz4320 8 months ago - 2 comments

#1112 - UniProt XML module code contribution

Issue - State: open - Opened by heuermh 10 months ago

#1111 - Adding safeguards when requesting chains from structure

Pull Request - State: open - Opened by josemduarte 10 months ago

#1110 - Upgrade to latest ciftools-java version

Pull Request - State: closed - Opened by josemduarte 10 months ago

#1109 - CIF parsing: entity type should be case insensitive

Pull Request - State: closed - Opened by josemduarte 10 months ago - 1 comment

#1108 - Parsing PDB-IHM CIF files

Pull Request - State: open - Opened by josemduarte 10 months ago

#1107 - ASA calculation should be done per model

Pull Request - State: closed - Opened by josemduarte 11 months ago

#1106 - More on lenient PDBx/mmCIF parsing

Pull Request - State: closed - Opened by josemduarte 11 months ago

#1105 - Update guava dependency version to 33.4.0-jre

Pull Request - State: open - Opened by heuermh 11 months ago

#1104 - Javadoc errors cleanup

Pull Request - State: closed - Opened by josemduarte 12 months ago

#1103 - More lenient CIF parsing

Pull Request - State: closed - Opened by josemduarte 12 months ago

#1102 - Website issue

Issue - State: open - Opened by ofluffydev about 1 year ago

#1101 - Fix CE-Symm bug with short repeats

Pull Request - State: closed - Opened by sbliven over 1 year ago

#1100 - Update guava dependency version to 33.3.0-jre

Pull Request - State: closed - Opened by heuermh over 1 year ago - 1 comment

#1099 - Removing functionality that uses mmtf.rcsb.org, now deprecated

Pull Request - State: closed - Opened by josemduarte over 1 year ago

#1098 - Fixing fatcat -alignPairs

Pull Request - State: open - Opened by josemduarte over 1 year ago

#1097 - BioJava Dependency issue could not resolve openchart:1.4.2

Issue - State: closed - Opened by curtishd over 1 year ago

#1096 - Issue of Biojava protein comparision tool

Pull Request - State: closed - Opened by B246371-2023 over 1 year ago - 2 comments
Labels: bug

#1094 - Upgrading to slf4j2

Pull Request - State: closed - Opened by josemduarte over 1 year ago - 1 comment

#1093 - Fix FastaStreamerTest tests failing on windows due to URL handling

Pull Request - State: closed - Opened by cometbroom over 1 year ago - 1 comment

#1092 - Biojava core tests fail on Windows

Issue - State: closed - Opened by jlerbsc over 1 year ago - 2 comments
Labels: bug

#1090 - Unable to find entrez (e -utilities) NCBI

Issue - State: open - Opened by kshitijgarg2609 over 1 year ago

#1089 - Fix container inefficiency in GenericFastaHeaderParser.java

Pull Request - State: closed - Opened by cinsttool almost 2 years ago - 7 comments

#1088 - Fix: refactor implementation and design smells

Pull Request - State: closed - Opened by cassandrabeaton almost 2 years ago

#1087 - Update guava dependency version to 33.1.0-jre

Pull Request - State: closed - Opened by heuermh almost 2 years ago - 1 comment

#1086 - Fix sonar issue 2629 Logging arguments should not require evaluation

Pull Request - State: closed - Opened by jlerbsc almost 2 years ago

#1085 - Replacing home-made copy by Files.copy

Pull Request - State: closed - Opened by josemduarte almost 2 years ago - 1 comment

#1084 - Replacing home-made copy by Files.copy

Pull Request - State: closed - Opened by josemduarte almost 2 years ago - 1 comment

#1083 - More lenient mmCIF parsing

Pull Request - State: closed - Opened by josemduarte almost 2 years ago

#1080 - Added Java Streaming I/O for FASTA Files

Pull Request - State: open - Opened by hilbertglm almost 2 years ago

#1078 - Update guava dependency version to 33.0.0-jre

Pull Request - State: closed - Opened by heuermh almost 2 years ago - 3 comments

#1077 - Changed the SCOP Installation URLs

Pull Request - State: closed - Opened by hilbertglm almost 2 years ago

#1077 - Changed the SCOP Installation URLs

Pull Request - State: closed - Opened by hilbertglm almost 2 years ago

#1076 - Updated to Jakarta JAXB and Java 17 (ref: #1075)

Pull Request - State: closed - Opened by hilbertglm about 2 years ago - 6 comments

#1076 - Updated to Jakarta JAXB and Java 17 (ref: #1075)

Pull Request - State: closed - Opened by hilbertglm about 2 years ago - 6 comments

#1075 - JAX-B Issues with Java 17

Issue - State: closed - Opened by hilbertglm about 2 years ago - 7 comments

#1073 - Dependency updates

Pull Request - State: closed - Opened by sjaenick about 2 years ago - 3 comments

#1071 - New release based on Java 17

Issue - State: closed - Opened by rizwan-ishtiaq over 2 years ago - 1 comment

#1070 - Fixing genbank export new line issue

Pull Request - State: closed - Opened by josemduarte over 2 years ago - 2 comments

#1069 - GenBank export producing spurious %n

Issue - State: closed - Opened by sjaenick over 2 years ago - 1 comment

#1064 - Update guava dependency version to 32.0.1-jre

Pull Request - State: closed - Opened by heuermh over 2 years ago - 1 comment

#1063 - Some more categories written out to CIF

Pull Request - State: closed - Opened by josemduarte over 2 years ago

#1062 - Fix Sonar S1130 throws declarations should not be superfluous

Pull Request - State: closed - Opened by jlerbsc over 2 years ago - 6 comments

#1061 - Suggestion: Sonar S1130 "throws" declarations should not be superfluous

Issue - State: open - Opened by jlerbsc over 2 years ago - 4 comments

#1060 - SonarQube bugs

Pull Request - State: closed - Opened by tmrpavan over 2 years ago - 13 comments

#1059 - Additional refactoring to maintain cohesion and solid principles.

Pull Request - State: closed - Opened by xcalibur91 over 2 years ago - 1 comment

#1059 - Additional refactoring to maintain cohesion and solid principles.

Pull Request - State: open - Opened by xcalibur91 over 2 years ago

#1057 - POM Cleanup: Add Maven descriptors & remove mention of Travis CI

Pull Request - State: closed - Opened by JonStargaryen almost 3 years ago - 3 comments

#1056 - More nullpdbid tests

Pull Request - State: closed - Opened by josemduarte almost 3 years ago

#1055 - Fixing issue with an edge case CIF parsing

Pull Request - State: closed - Opened by josemduarte almost 3 years ago

#1053 - Upgrading source and target to java 11

Pull Request - State: closed - Opened by josemduarte almost 3 years ago - 7 comments

#1052 - Sonar S4973 '==' and '!=' should not be used when 'equals' is overridden

Pull Request - State: closed - Opened by jlerbsc almost 3 years ago - 13 comments

#1051 - Sonar S4973 "==" and "!=" should not be used when "equals" is overridden

Issue - State: closed - Opened by jlerbsc almost 3 years ago - 4 comments

#1050 - Bump dependency ciftools-java-jdk8 to 4.0.5

Pull Request - State: closed - Opened by aalhossary almost 3 years ago

#1048 - Q: How can I print the 3-letter protein sequence?

Issue - State: closed - Opened by DominantDuck about 3 years ago - 3 comments

#1047 - [SECURITY] Fix Temporary File Information Disclosure Vulnerability

Pull Request - State: closed - Opened by JLLeitschuh about 3 years ago - 1 comment

#1046 - [SECURITY] Fix Temporary File Information Disclosure Vulnerability

Pull Request - State: closed - Opened by JLLeitschuh about 3 years ago - 6 comments

#1045 - Keep ciftools up-to-date

Pull Request - State: closed - Opened by JonStargaryen about 3 years ago

#1044 - Switching to new DNS name for wwpdb http file server

Pull Request - State: closed - Opened by josemduarte about 3 years ago

#1043 - Update CHANGELOG.md

Pull Request - State: closed - Opened by jamesmorris about 3 years ago

#1042 - GenBankWriter does not use information in the original header #942

Pull Request - State: closed - Opened by jamesmorris about 3 years ago - 2 comments

#1041 - [SECURITY] Use HTTPS to resolve dependencies in Gradle Build

Pull Request - State: closed - Opened by JLLeitschuh over 3 years ago - 3 comments

#1040 - GitHub Workflows security hardening

Pull Request - State: closed - Opened by sashashura over 3 years ago

#1039 - Aromaticity calculation (Protein) #1037

Pull Request - State: closed - Opened by simoesrenato over 3 years ago - 4 comments

#1038 - Test Smell: it is not a good test practice to use the loop in the test

Issue - State: open - Opened by TestSmell over 3 years ago - 4 comments

#1037 - Aromaticity calculation (Protein)

Issue - State: closed - Opened by simoesrenato over 3 years ago - 3 comments

#1036 - Fix local align score vector

Pull Request - State: closed - Opened by aegugup over 3 years ago - 3 comments

#1035 - New release based on Java 11

Issue - State: closed - Opened by josemduarte over 3 years ago - 13 comments

#1034 - #886 String Formatter error when key or value of Qualifier has character "%"

Pull Request - State: closed - Opened by jamesmorris over 3 years ago - 2 comments

#1031 - Update URL of Assembly CIF File in TestURLBasedFileParsing

Pull Request - State: closed - Opened by JonStargaryen over 3 years ago

#1030 - Update ciftools-java-jdk8 Dependency

Pull Request - State: closed - Opened by JonStargaryen over 3 years ago

#1029 - Prevent XXE (Xml eXternal Entity) injection when parsing XML data

Pull Request - State: closed - Opened by marty-rabens over 3 years ago

#1028 - Calculating Ramachandran Angles from a PDB File

Issue - State: closed - Opened by LobsterMan123 over 3 years ago - 4 comments
Labels: question

#1027 - Update guava dependency version to 31.1-jre

Pull Request - State: closed - Opened by heuermh almost 4 years ago - 1 comment

#1026 - Refactor

Pull Request - State: closed - Opened by zilsemaj almost 4 years ago - 1 comment

#1025 - How to align any two protein and get their TM-score

Issue - State: closed - Opened by dabianzhixing almost 4 years ago - 1 comment
Labels: question

#1024 - Add file download validation

Pull Request - State: closed - Opened by aalhossary almost 4 years ago

#1023 - Fix #929

Pull Request - State: closed - Opened by zedomel almost 4 years ago

#1022 - fixes biojava/biojava#910 for network flaky tests

Pull Request - State: closed - Opened by unshorn almost 4 years ago

#1021 - Additional tests of null PDBIds

Pull Request - State: closed - Opened by sbliven almost 4 years ago - 1 comment

#1020 - Handling some nulls in PdbId creation

Pull Request - State: closed - Opened by josemduarte almost 4 years ago - 2 comments

#1019 - Null pdb ids are not handled correctly in a few places

Issue - State: closed - Opened by josemduarte almost 4 years ago
Labels: bug

#1018 - Harmonize Profile and LightweightProfile

Issue - State: open - Opened by sbliven almost 4 years ago

#1017 - Improve MAVEN build Performance

Pull Request - State: closed - Opened by SilverSteven almost 4 years ago - 2 comments

#1016 - o.b.n.core.sequence.CDSSequence doesn't reverse-complement correctly

Issue - State: open - Opened by richarda23 about 4 years ago
Labels: bug

#1015 - Bump log4j-api from 2.17.0 to 2.17.1

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#1014 - Bump log4j-core from 2.17.0 to 2.17.1

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies