Release 3.4.0

• Rewrite of REST service as a Spring app with MongoDB as backend.
• Adaptation of CLI to new needs of backend
• Removal of GWT-based web UI

Release 3.2.3

• Bugfix: now pointing to the right cif.gz file in 3D lattice graph view in WUI. It broke when upgrading to jetty 9.4
• Other small bug fixes
• Upgrade to latest UniProt japi
• Upgrade to latest BioJava 5.3.0. Some PDB parsing bugfixes with it

Release 3.2.2

• All packages but eppic-wui now compile under JRE 11 javac
• Moved orm.xml to jpa annotations
• Remove gridengine dependency for web server. New native java implementation of a queuing system
• Alive endpoint now checks that disk is not full

Release 3.2.1

• Better REST API docs
• Upgrade to latest openapi version for REST API docs
• Some bug fixes

Release 3.2.0

• mmseqs2 replaces blast in sequence search for precomputation, dramatically reducing time needed for PDB precomputation #46
• mmseqs2 replaces blastclust for redundancy elimination clustering. Removes blastclust dependency
• a single run of redundancy elimination with clustering at 90% seq id is now used (instead of incrementally trying different sequence identities)
• extracted utils into new module eppic-util
• pdb to uniprot reference alignment now strictly from SIFTS #188
• all insertion/deletions are now not considered for evolutionary analysis
• no evolutionary analysis performed for peptides (30 default length cutoff). Solves #9, #5
• keeps blastp for user jobs. Mmseqs is not fast for single jobs (unless setup with a server holding the indices in memory)
• user jobs use uniprot japi instead of local uniprot db
• sequence search cache (before blast cache) is now in db (via JPA)
• local uniprot db is now interfaced via JPA instead of raw sql. DB interface now fully JPA
• improvements in precomputation scripts to support mmseqs

Release 3.1.0

• New REST API, more data in downloads and more fine grained control of data to download
• Database contains all graph data and all symmetry operators data
• Upgraded to BioJava 5.1.0 solving a few issues
• More efficient precomputation: no need to store coordinate files anymore, servlet creates them on the fly from data in db
• Parallel UploadToDb with -n
• Better layout of project with clearer package names
• Fixed issue #184
• Fixed issue #219
• Fixed issue #209

Release 3.0.6

• Upgrade to BioJava 5.0.1
• Hibernate latest bugfix release, fixed some dependencies
• Better ClusterSequences script

Release 3.0.5

• Upgraded to next BioJava major release 5.0.0
• Fixed issues #206, #212, #141, #205, #101
• Sequence clusters with mmseqs2
• New publication added

Release 3.0.4

• Now normalising assembly probabilities
• Updated to latest hibernate versions
• Structures with many clashes in any interface are now fully computed, showing warnings for the clashes
• Updated to latest UniProt JAPI, the UniProt connection in CLI wasn't working
• Fixed issue #200 upgrading to BioJava 4.2.10
• Improvements in CLI for precomputation, improvements in db tools

Release 3.0.3

• Updated to BioJava 4.2.9
• Fixed issue #195
• Fixed issue #196
• Fixed issue #155
• Fixed issue #175
• Some fixes related to graph contraction, see #197
• Fixed issue with NGL not displaying all subassemblies in disjoint cases, see #101