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Wednesday 17 Feb
5:16 pm

Jim Procter

JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

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    ./EmblFlatFile.java
4:08 pm

Jim Procter

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

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    • +62
    ./EmblFlatFile.java
Wednesday 03 Feb
4:34 pm

Jim Procter

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

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    ./gff/ExonerateHelper.java
Monday 14 Dec 2020
7:58 pm

Jim Procter

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

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    ./CountReader.java
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    ./FileFormat.java
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    ./FileLoader.java
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    ./IdentifyFile.java
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    ./SequenceAnnotationReport.java
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    ./StockholmFile.java
  7. … 51 more files in changeset.
Saturday 12 Dec 2020
2:39 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

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    ./FileLoader.java
  2. … 5 more files in changeset.
Friday 11 Dec 2020
9:04 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3785 set full title on automatically opened Overview windows

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    ./FileLoader.java
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Friday 04 Dec 2020
5:35 pm

Ben Soares

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.

5:31 pm

Ben Soares

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.

Wednesday 02 Dec 2020
5:56 pm

Jim Procter

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.

5:53 pm

Jim Procter

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 ?

5:20 pm

Jim Procter

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
Friday 20 Nov 2020
1:04 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3779 apply properties to all groups with given name, not just first

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    ./AnnotationFile.java
  2. … 1 more file in changeset.
11:59 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3761 extra check that VCF feature is fully mappable to sequence

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    ./vcf/VCFLoader.java
Friday 13 Nov 2020
6:09 pm

Ben Soares

JAL-3775 Eclipse re-formatting commit

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    ./BackupFiles.java
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Thursday 12 Nov 2020
2:36 pm

Jim Procter

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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    ./vcf/VCFLoader.java
  2. … 1 more file in changeset.
Wednesday 28 Oct 2020
10:56 pm

Jim Procter

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)

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    ./EmblFlatFile.java
Thursday 17 Sep 2020
12:19 pm

Jim Procter

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

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    ./JSONFile.java
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Thursday 10 Sep 2020
3:27 pm

Ben Soares

JAL-3744 this obvious attempt to detect/gunzip file input for jalviewjs fails

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    ./FileParse.java
Thursday 27 Aug 2020
4:02 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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    ./SequenceAnnotationReport.java
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4:02 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3725 restrict mapped virtual feature location to mapped region

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    ./SequenceAnnotationReport.java
  2. … 4 more files in changeset.
Friday 21 Aug 2020
11:45 am

Jim Procter

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

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    ./FileParse.java
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11:37 am

Jim Procter

JAL-3615 code tidy, improve unit test

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    ./FileParse.java
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Thursday 20 Aug 2020
2:55 pm

Ben Soares

JAL-2656 better read of (potential) gzip magic bytes

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    ./FileParse.java
Tuesday 18 Aug 2020
5:07 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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    ./FileParse.java
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3:32 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1260 refactored multi-line qualifier separators

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    ./FlatFile.java
2:59 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3692 parse multiline CDS location correctly

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    ./EmblFlatFile.java
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2:22 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

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    ./FileFormat.java
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    ./FlatFile.java
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    ./IdentifyFile.java
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1:05 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1260 refactored GenBank (and EMBL) flat file parser

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    ./EmblFlatFile.java
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    ./FlatFile.java
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    ./GenBankFile.java
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Monday 17 Aug 2020
3:53 pm

Jim Procter

JAL-3490 don't init the combo box's history cache for JS execution

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    ./cache/JvCacheableInputBox.java
1:53 pm

Jim Procter

JAL-3490 merged with 2.11.2 develop

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    ./cache/JvCacheableInputBox.java
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