jalview

Clone Tools

Stats

Commits this week: 26
Total Committers: 69
Last Commit:
Commits this week: 26

Lines of code count not available

Commit Activity

Commits By Day In Week
52 week commits volume
Commits By Day In Week
Commits by day
Commits By Day In Week
Commits by hour
Commits By Hour In Day
Commit calendar
 

Most active committers (90 days)

loading
loading
  • last updated a few seconds ago
All Commits Reviews
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Friday 04 Dec
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
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
Tuesday 20 Oct
5:23 pm

Jim Procter

JAL-3765 fix test

Options
    • -10
    • +13
    /test/jalview/analysis/FinderTest.java
5:13 pm

Jim Procter

fix for JAL-3765

Options
    • -1
    • +1
    /src/jalview/analysis/Finder.java
Monday 19 Oct
6:07 pm

Jim Procter

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

Options
    • -0
    • +10
    /test/jalview/analysis/FinderTest.java
Friday 25 Sep
9:39 am

Ben Soares

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

Options
    • -1
    • +2
    /gradle.properties
8:16 am

Jim Procter

JAL-3758 tweak what’s new for 2.11.1.2!

Options
    • -5
    • +6
    /help/help/html/whatsNew.html
8:05 am

Jim Procter

JAL-3758 release Fri 25th Sep

Options
    • -1
    • +1
    /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

Options
Thursday 24 Sep
6:16 pm

Ben Soares

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

Options
    • -1
    • +1
    /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

Options
    • -1
    • +1
    /RELEASE
    • -0
    • +18
    /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 !)

Options
    • -6
    • +1
    /src/jalview/bin/Jalview.java
Wednesday 23 Sep
11:41 pm

Ben Soares

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

Options
    • -1
    • +2
    /src/jalview/bin/Jalview.java
Thursday 17 Sep
1:38 pm

Jim Procter

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

Options
    • -0
    • +8
    /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

Options
12:19 pm

Jim Procter

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

Options
    • -1
    • +1
    /help/help/html/features/commandline.html
    • -4
    • +4
    /help/help/html/features/groovy.html
    • -4
    • +4
    /help/help/html/features/jvlfiles.html
    • -1
    • +1
    /help/help/html/groovy/featuresCounter.html
    • -2
    • +2
    /help/help/html/index.html
    • -1
    • +1
    /help/help/html/memory.html
    • -3
    • +3
    /help/help/html/webServices/newsreader.html
    • -3
    • +3
    /src/jalview/bin/Cache.java
    • -6
    • +9
    /src/jalview/bin/Jalview.java
    • -1
    • +1
    /src/jalview/gui/BlogReader.java
    • -4
    • +4
    /src/jalview/gui/Desktop.java
    • -2
    • +2
    /src/jalview/gui/Preferences.java
    • -1
    • +1
    /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

Options
    • -3
    • +5
    /src/jalview/bin/Jalview.java
11:35 am

Jim Procter

JAL-3675 patch release date 17th September 2020

Options
    • -1
    • +1
    /help/help/html/releases.html
Wednesday 16 Sep
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
6:05 pm

Jim Procter

JAL-3675 logged JAL-3748 as known defect

Options
    • -0
    • +6
    /help/help/html/releases.html
4:48 pm

Jim Procter

JAL-3765 JAL-3718 release notes

Options
    • -1
    • +8
    /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

Options
4:17 pm

Ben Soares

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

Options
    • -1
    • +1
    /getdown/lib/FJVL_VERSION
    • -1
    • +1
    /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