jalview

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Commits this week: 5
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Commits this week: 5

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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
Monday 19 Oct 2020
11:59 am

Jim Procter

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

Tuesday 29 Sep 2020
4:41 pm

Jim Procter

JAL-3760 fix tests for changed behaviour

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    /test/jalview/util/ComparisonTest.java
3:26 pm

Jim Procter

JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like

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    /src/jalview/util/Comparison.java
Friday 25 Sep 2020
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

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    /gradle.properties
8:16 am

Jim Procter

JAL-3758 tweak what’s new for 2.11.1.2!

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    /help/help/html/whatsNew.html
8:05 am

Jim Procter

JAL-3758 release Fri 25th Sep

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    /help/help/html/releases.html
7:45 am

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

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Thursday 24 Sep 2020
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

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    /build.gradle
2:49 pm

Jim Procter

2:49 pm

Jim Procter

2:48 pm

Jim Procter

2:39 pm

Jim Procter

JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings
2:38 pm

Jim Procter

JAL-3758 2.11.1.2 patch release notes and version bump

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    /RELEASE
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    /help/help/html/releases.html
2:36 pm

Jim Procter

JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

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    /src/jalview/bin/Jalview.java
Wednesday 23 Sep 2020
11:41 pm

Ben Soares

JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://

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    /src/jalview/bin/Jalview.java
Thursday 17 Sep 2020
1:38 pm

Jim Procter

JAL-3675 release notes for JAL-3750 JAL-3751

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    /help/help/html/releases.html
12:28 pm

Jim Procter

Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

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12:19 pm

Jim Procter

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

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    /help/help/html/features/commandline.html
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    /help/help/html/features/groovy.html
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    /help/help/html/features/jvlfiles.html
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    /help/help/html/groovy/featuresCounter.html
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    /help/help/html/index.html
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    /help/help/html/memory.html
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    /help/help/html/webServices/newsreader.html
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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/BlogReader.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/io/JSONFile.java
12:09 pm

Jim Procter

JAL-3750 parse protocol before checking if argument to -open can be opened as a file

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    /src/jalview/bin/Jalview.java
11:35 am

Jim Procter

JAL-3675 patch release date 17th September 2020

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    /help/help/html/releases.html
Wednesday 16 Sep 2020
6:47 am

Jim Procter

JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
Tuesday 15 Sep 2020
6:05 pm

Jim Procter

JAL-3675 logged JAL-3748 as known defect

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    /help/help/html/releases.html
4:48 pm

Jim Procter

JAL-3765 JAL-3718 release notes

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    /help/help/html/releases.html

changeset discussion

  1. Jim Procter: not related to JAL-3765 ! Actually related to JAL-3675!
4:34 pm

Jim Procter

Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

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4:17 pm

Ben Soares

JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

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    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar