Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

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

  1. … 51 more files in changeset.
JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

  1. … 5 more files in changeset.
JAL-3785 set full title on automatically opened Overview windows

  1. … 1 more file in changeset.
Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agree this is just touching on a much bigger task. However... The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview...

Agree this is just touching on a much bigger task.
However...
The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly u...

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS,...

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS, so probably not a dealbreaker. Do you agree ?

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
JAL-3779 apply properties to all groups with given name, not just first

  1. … 1 more file in changeset.
JAL-3761 extra check that VCF feature is fully mappable to sequence

JAL-3775 Eclipse re-formatting commit

  1. … 5 more files in changeset.
Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

  1. … 1 more file in changeset.
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)

JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

  1. … 12 more files in changeset.
JAL-3744 this obvious attempt to detect/gunzip file input for jalviewjs fails

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-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

  1. … 1 more file in changeset.
JAL-3615 code tidy, improve unit test

  1. … 1 more file in changeset.
JAL-2656 better read of (potential) gzip magic bytes

JAL-2656 Java 8 compatible test for gzipped, refactored for unit test

  1. … 1 more file in changeset.
JAL-1260 refactored multi-line qualifier separators

JAL-3692 parse multiline CDS location correctly

  1. … 2 more files in changeset.
JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

  1. … 3 more files in changeset.
JAL-1260 refactored GenBank (and EMBL) flat file parser

    • -0
    • +207
    ./GenBankFile.java
  1. … 5 more files in changeset.
JAL-3490 don't init the combo box's history cache for JS execution

JAL-3490 merged with 2.11.2 develop

  1. … 22 more files in changeset.