biojava/biojava (org.biojava:biojava-structure)
### [`v6.1.0`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-610)
\==============================
##### Added
- GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information
- GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space
- GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID
- Aromaticity calculation in biojava-aa-prop module
##### Fixed
- GenBankWriter - String Formatter error when key or value of Qualifier has character "%", [#886](https://togithub.com/biojava/biojava/issues/886)
- GenBankWriter - outputting db_xref feature qualifiers
- GenBankWriter - outputting the accession version and GI ID
- GenBankWriter - outputting feature locations containing joins and partial locations
- GenBankReader - reading locations split over multiple lines
- GenBankReader - set if feature qualifier values require quotes
- Local alignment with linear gap penalty was producing an NPE, [#1036](https://togithub.com/biojava/biojava/issues/1036)
- New default server for PDB files. Note that from Aug 2023 older versions of BioJava will
not be able to fetch PDB files unless PDB.FILE.SERVER system property is used to override
the default server
- Dependency upgrades
- Some bug and security fixes
### [`v6.0.5`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-605)
\==============================
##### Fixed
- Null handling in a few places related to loading PDB, CIF, mmtf files (issue introduced in 6.0.0). [#1019](https://togithub.com/biojava/biojava/issues/1019)
### [`v6.0.4`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-604)
\==============================
##### Fixed
- Log4j dependency upgraded to 2.17.1 to avoid new vulnerabilities
- Some new tests
- Fixes in tests and docs
- Bugfix in LocalProteinDomainParser [#1009](https://togithub.com/biojava/biojava/issues/1009)
### [`v6.0.3`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-603)
\==============================
##### Fixed
- Log4j dependency upgraded to 2.16.0, to avoid log4hshell vulnerability
### [`v6.0.2`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-602)
\==============================
##### Fixed
- Log4j dependency upgraded to 2.15.0, to avoid log4hshell vulnerability
- PDB and mmCIF resolution parsing fixes. [#1000](https://togithub.com/biojava/biojava/issues/1000)
### [`v6.0.1`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-601)
\==============================
##### Fixed
- Now actually runnable in a java-8 JRE. Previous release 6.0.0 had a java-11 dependency that made it incompatible. [#996](https://togithub.com/biojava/biojava/issues/996)
- Switch JAXB to glassfish implementation for better java 15+ support. Now biojava should run under a java-15 JRE. [#996](https://togithub.com/biojava/biojava/issues/996)
### [`v6.0.0`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-600)
\==============================
Note that BioJava 6.0.0 was intended as java-8 runtime compatible. However, a java-11 dependency crept in making it java-8 incompatible. Please use 6.0.1 instead.
##### Removed
- All code related to All-vs-All structural alignments db calculation and access
- JFatCatClient and all code depending on it
- PDP domain providers (depended on JFatCatClient)
- Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO)
- RemoteScopInstallation consuming data provided by source.rcsb.org
- The whole `org.biojava.nbio.structure.rcsb` package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020)
- The whole `org.biojava.nbio.structure.validation` package
- The `org.biojava.nbio.structure.domain.PDBDomainProvider` class to pull domain definitions from legacy RCSB PDB APIs
- Support for automatically fetching dssp files from RCSB (`org.biojava.nbio.structure.secstruc.DSSPParser.fetch()`)
- `org.biojava.nbio.structure.PDBStatus`: simplified `Status` enum to 3 states, with OBSOLETE now called REMOVED
- `org.biojava.nbio.structure.PDBStatus`: removed `getReplacement` and `getReplaces`
- Removed `org.biojava.nbio.structure.io.mmcif` package
- Removed functionality to write isolated CIF headers from `FileConvert`
- Removed `org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()`
- Removed from `org.biojava.nbio.structure.Chain` interface: `getParent()`, `setParent()`, `getAtomLigands()`, `getSwissprotId()`, `setSwissprotId()`, `getInternalChainID()`, `setInternalChainID()`, `getChainID()`, `setChainID()`
- Removed from `org.biojava.nbio.structure.Structure` interface: `findChain()`, `getId()`, `setId()`, `getChainByPDB()`, `getCompoundById()`, `getResidueRanges()`, `getRanges()`
- Removed from `org.biojava.nbio.structure.StructureTools` : `isNucleicAcid()`, `isProtein()`, `getPredominantGroupType()`, `isChainWaterOnly()`, `isChainPureNonPolymer()`, `getReducedStructure()`
- Removed `org.biojava.nbio.structure.io.SandboxStyleStructureProvider`
- In `org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser` made all methods private except `parseXMLfile`
##### Breaking API changes
- Extracted `StructureIO.StructureFiletype` enum to `org.biojava.nbio.structure.io.StructureFiletype` (supports `PDB`, `MMTF`, `CIF`, and `BCIF`)
- `org.biojava.nbio.structure.align.util.AtomCache`: removed `setUseMmCif`, `setUseMmtf`, `isUseMmCif`, and `isUseMmtf` - replaced by `setFiletype` and `getFiletype` that controls parsed content via the `StructureFiletype`
- `org.biojava.nbio.structure.io.MMCIFFileReader` is now effectively `org.biojava.nbio.structure.io.CifFileReader`
- Moved `org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord` to `org.biojava.nbio.structure.DatabasePDBRevRecord.java`
- Moved all chem-comp model classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.chem`
- Moved all chem-comp parsing classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.io.cif`
- Moved classes in `org.biojava.nbio.structure.io.mmcif` to `org.biojava.nbio.structure.chem`
- Fixed `CRC64Checksum#public void update(byte[] b, int offset, int length)` to use the `length` argument correctly as specified in `java.util.zip.Checksum` interface.
- In `SubstructureIdentifier`, `StructureName`, `EcodDomain`, `ScopDomain` : `getPdbId()` returns `PdbId` object instead of `String`.
- Removed `DownloadChemCompProvider.useDefaultUrlLayout` with a more flexible system to provide templated URLs `DownloadChemCompProvider.setChemCompPathUrlTemplate()` and `DownloadChemCompProvider.setServerBaseUrl()`
- In `Structure` (and `StructureImple`), the accessor methods `String getPdbId()` and `setPdbId(String)` were previously depricated. They were revived in BioJava 6.0.0 but as `PdbId getPdbId()` and `setPdbId(PdbId)` instead.n
- `GeneSequence#public ExonSequence addExon(AccessionID accession, int begin, int end)` no longer declares a checked exception [#966](https://togithub.com/biojava/biojava/issues/966)
##### Added
- New `keywords` field in `PDBHeader` class, populated by PDB and mmCIF parsers [#946](https://togithub.com/biojava/biojava/issues/946)
- OBO parsing now supports multiple altids, [#960](https://togithub.com/biojava/biojava/issues/960)
- New class `PdbId` that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format [#930](https://togithub.com/biojava/biojava/issues/930)
##### Fixed
- Correct chain assignment to entities when parsing PDB/mmCIF without entity information (in cases with more than 3 chains per entity) [#931](https://togithub.com/biojava/biojava/issues/931)
- Dealing with chain ids correctly when parsing bonds in PDB-format files [#943](https://togithub.com/biojava/biojava/issues/943) [#929](https://togithub.com/biojava/biojava/issues/929)
[ ] If you want to rebase/retry this PR, check this box
This PR contains the following updates:
6.0.0-alpha2->6.1.0By merging this PR, the issue #6 will be automatically resolved and closed:
Release Notes
biojava/biojava (org.biojava:biojava-structure)
### [`v6.1.0`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-610) \============================== ##### Added - GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information - GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space - GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID - Aromaticity calculation in biojava-aa-prop module ##### Fixed - GenBankWriter - String Formatter error when key or value of Qualifier has character "%", [#886](https://togithub.com/biojava/biojava/issues/886) - GenBankWriter - outputting db_xref feature qualifiers - GenBankWriter - outputting the accession version and GI ID - GenBankWriter - outputting feature locations containing joins and partial locations - GenBankReader - reading locations split over multiple lines - GenBankReader - set if feature qualifier values require quotes - Local alignment with linear gap penalty was producing an NPE, [#1036](https://togithub.com/biojava/biojava/issues/1036) - New default server for PDB files. Note that from Aug 2023 older versions of BioJava will not be able to fetch PDB files unless PDB.FILE.SERVER system property is used to override the default server - Dependency upgrades - Some bug and security fixes ### [`v6.0.5`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-605) \============================== ##### Fixed - Null handling in a few places related to loading PDB, CIF, mmtf files (issue introduced in 6.0.0). [#1019](https://togithub.com/biojava/biojava/issues/1019) ### [`v6.0.4`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-604) \============================== ##### Fixed - Log4j dependency upgraded to 2.17.1 to avoid new vulnerabilities - Some new tests - Fixes in tests and docs - Bugfix in LocalProteinDomainParser [#1009](https://togithub.com/biojava/biojava/issues/1009) ### [`v6.0.3`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-603) \============================== ##### Fixed - Log4j dependency upgraded to 2.16.0, to avoid log4hshell vulnerability ### [`v6.0.2`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-602) \============================== ##### Fixed - Log4j dependency upgraded to 2.15.0, to avoid log4hshell vulnerability - PDB and mmCIF resolution parsing fixes. [#1000](https://togithub.com/biojava/biojava/issues/1000) ### [`v6.0.1`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-601) \============================== ##### Fixed - Now actually runnable in a java-8 JRE. Previous release 6.0.0 had a java-11 dependency that made it incompatible. [#996](https://togithub.com/biojava/biojava/issues/996) - Switch JAXB to glassfish implementation for better java 15+ support. Now biojava should run under a java-15 JRE. [#996](https://togithub.com/biojava/biojava/issues/996) ### [`v6.0.0`](https://togithub.com/biojava/biojava/blob/HEAD/CHANGELOG.md#BioJava-600) \============================== Note that BioJava 6.0.0 was intended as java-8 runtime compatible. However, a java-11 dependency crept in making it java-8 incompatible. Please use 6.0.1 instead. ##### Removed - All code related to All-vs-All structural alignments db calculation and access - JFatCatClient and all code depending on it - PDP domain providers (depended on JFatCatClient) - Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO) - RemoteScopInstallation consuming data provided by source.rcsb.org - The whole `org.biojava.nbio.structure.rcsb` package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020) - The whole `org.biojava.nbio.structure.validation` package - The `org.biojava.nbio.structure.domain.PDBDomainProvider` class to pull domain definitions from legacy RCSB PDB APIs - Support for automatically fetching dssp files from RCSB (`org.biojava.nbio.structure.secstruc.DSSPParser.fetch()`) - `org.biojava.nbio.structure.PDBStatus`: simplified `Status` enum to 3 states, with OBSOLETE now called REMOVED - `org.biojava.nbio.structure.PDBStatus`: removed `getReplacement` and `getReplaces` - Removed `org.biojava.nbio.structure.io.mmcif` package - Removed functionality to write isolated CIF headers from `FileConvert` - Removed `org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()` - Removed from `org.biojava.nbio.structure.Chain` interface: `getParent()`, `setParent()`, `getAtomLigands()`, `getSwissprotId()`, `setSwissprotId()`, `getInternalChainID()`, `setInternalChainID()`, `getChainID()`, `setChainID()` - Removed from `org.biojava.nbio.structure.Structure` interface: `findChain()`, `getId()`, `setId()`, `getChainByPDB()`, `getCompoundById()`, `getResidueRanges()`, `getRanges()` - Removed from `org.biojava.nbio.structure.StructureTools` : `isNucleicAcid()`, `isProtein()`, `getPredominantGroupType()`, `isChainWaterOnly()`, `isChainPureNonPolymer()`, `getReducedStructure()` - Removed `org.biojava.nbio.structure.io.SandboxStyleStructureProvider` - In `org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser` made all methods private except `parseXMLfile` ##### Breaking API changes - Extracted `StructureIO.StructureFiletype` enum to `org.biojava.nbio.structure.io.StructureFiletype` (supports `PDB`, `MMTF`, `CIF`, and `BCIF`) - `org.biojava.nbio.structure.align.util.AtomCache`: removed `setUseMmCif`, `setUseMmtf`, `isUseMmCif`, and `isUseMmtf` - replaced by `setFiletype` and `getFiletype` that controls parsed content via the `StructureFiletype` - `org.biojava.nbio.structure.io.MMCIFFileReader` is now effectively `org.biojava.nbio.structure.io.CifFileReader` - Moved `org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord` to `org.biojava.nbio.structure.DatabasePDBRevRecord.java` - Moved all chem-comp model classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.chem` - Moved all chem-comp parsing classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.io.cif` - Moved classes in `org.biojava.nbio.structure.io.mmcif` to `org.biojava.nbio.structure.chem` - Fixed `CRC64Checksum#public void update(byte[] b, int offset, int length)` to use the `length` argument correctly as specified in `java.util.zip.Checksum` interface. - In `SubstructureIdentifier`, `StructureName`, `EcodDomain`, `ScopDomain` : `getPdbId()` returns `PdbId` object instead of `String`. - Removed `DownloadChemCompProvider.useDefaultUrlLayout` with a more flexible system to provide templated URLs `DownloadChemCompProvider.setChemCompPathUrlTemplate()` and `DownloadChemCompProvider.setServerBaseUrl()` - In `Structure` (and `StructureImple`), the accessor methods `String getPdbId()` and `setPdbId(String)` were previously depricated. They were revived in BioJava 6.0.0 but as `PdbId getPdbId()` and `setPdbId(PdbId)` instead.n - `GeneSequence#public ExonSequence addExon(AccessionID accession, int begin, int end)` no longer declares a checked exception [#966](https://togithub.com/biojava/biojava/issues/966) ##### Added - New `keywords` field in `PDBHeader` class, populated by PDB and mmCIF parsers [#946](https://togithub.com/biojava/biojava/issues/946) - OBO parsing now supports multiple altids, [#960](https://togithub.com/biojava/biojava/issues/960) - New class `PdbId` that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format [#930](https://togithub.com/biojava/biojava/issues/930) ##### Fixed - Correct chain assignment to entities when parsing PDB/mmCIF without entity information (in cases with more than 3 chains per entity) [#931](https://togithub.com/biojava/biojava/issues/931) - Dealing with chain ids correctly when parsing bonds in PDB-format files [#943](https://togithub.com/biojava/biojava/issues/943) [#929](https://togithub.com/biojava/biojava/issues/929)