datamodel

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-2909 pass a dummy sequence object to receive features. Ideally we should test that features look like they are expected too here !

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

  1. … 101 more files in changeset.
JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

  1. … 3 more files in changeset.
JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

  1. … 2 more files in changeset.
JAL-2226 new method to search for annotation matching particular description as well as calcId and label

  1. … 2 more files in changeset.
JAL-3863 promote non-canonical version of dbref to a canonical one

  1. … 1 more file in changeset.
JAL-3863 passing test to verify a uniprot accession with canonical flag set is transferred via the DBRefFetcher (and the SequenceI.transferAnnotation method it calls)

  1. … 3 more files in changeset.
patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-3840 failing test - show that addGaps overflows

  1. … 1 more file in changeset.
JAL-3840 failing test - show that addGaps overflows

  1. … 1 more file in changeset.
JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

  1. … 56 more files in changeset.
JAL-3763 Javadoc, check for null, additional tests

  1. … 2 more files in changeset.
JAL-3763 Javadoc, check for null, additional tests

  1. … 2 more files in changeset.
JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

  1. … 2 more files in changeset.
JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

  1. … 2 more files in changeset.
JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences

JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

JAL-3700 additions and corrections to unit tests (trivial) Conflicts: test/jalview/util/MappingUtilsTest.java

  1. … 2 more files in changeset.
JAL-3700 additions and corrections to unit tests

  1. … 2 more files in changeset.
JAL-3576 unit test for preserving order of colocated features

JAL-3725 restrict mapped virtual feature location to mapped region Conflicts: src/jalview/gui/PopupMenu.java

  1. … 4 more files in changeset.
JAL-3725 restrict mapped virtual feature location to mapped region

  1. … 4 more files in changeset.
JAL-3725 restrict mapped virtual feature location to mapped region

  1. … 4 more files in changeset.
JAL-3490 merged with 2.11.2 develop

  1. … 22 more files in changeset.
JAL-3706 handle e.g. mapped exon feature extending beyond mapped range

  1. … 1 more file in changeset.