jalview/src/jalview

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Friday 01 Oct
5:36 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3616 show name of structure viewer in ‘new view’ button

Options
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    • +5
    ./GStructureChooser.java
  2. … 2 more files in changeset.
12:28 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

Options
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    • +19
    ./GStructureChooser.java
  2. … 2 more files in changeset.
Friday 24 Sep
5:23 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

Options
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    • +2
    ./GStructureChooser.java
  2. … 3 more files in changeset.
2:19 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 right click to view popup menu to show link - maybe better to have a link button in the table instead ?

Options
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    • +31
    ./GStructureChooser.java
  2. … 1 more file in changeset.
Tuesday 14 Sep
10:52 am

Ben Soares

JAL-2422 More helpful highlighting/user guidance of missing structure viewer path

Options
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    • +13
    ./GPreferences.java
  2. … 2 more files in changeset.
Monday 13 Sep
4:02 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 select single best TDB structure and select structures from particular provider (this code is horrific !)

Options
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    • +25
    ./FilterOption.java
  2. … 4 more files in changeset.
Saturday 11 Sep
11:53 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 patch failing tests and todo for future

Options
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    • +1
    ./GStructureChooser.java
  2. … 2 more files in changeset.
Friday 10 Sep
3:06 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box

Options
    • -1
    • +13
    ./FilterOption.java
  2. … 4 more files in changeset.
Friday 03 Sep
3:33 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 refactored FilterOption provider to the StructureChooserQuerySource implementation - implementation now is completely independent of GUI code.

Options
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    ./FilterOption.java
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    ./GStructureChooser.java
  3. … 5 more files in changeset.
Thursday 26 Aug
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 pulled out more of the FTS dependent parts of structurechooser

Options
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    • +11
    ./GStructureChooser.java
  2. … 2 more files in changeset.
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 pulled out more of the FTS dependent parts of structurechooser

Options
    • -7
    • +11
    ./GStructureChooser.java
  2. … 2 more files in changeset.
Sunday 25 Jul
4:08 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3848 slivka preferences in javascript

Options
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    • +3
    ./GPreferences.java
Tuesday 06 Jul
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Friday 19 Mar
11:18 pm

Ben Soares

JAL-3503 missed a widget being disabled

Options
    • -0
    • +1
    ./GPreferences.java
10:53 pm

Ben Soares

JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

Options
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    • +322
    ./GPreferences.java
  2. … 20 more files in changeset.
Friday 05 Mar
11:24 am

Ben Soares

JAL-3618 Enable appBundleIsTraversable in JFileChooser on macOS

Options
    • -0
    • +8
    ./GPreferences.java
Monday 11 Jan
5:08 pm

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

JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

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    • +14
    ./GAlignFrame.java
  2. … 4 more files in changeset.
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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    ./GAlignFrame.java
    • -15
    • +18
    ./GPreferences.java
  3. … 55 more files in changeset.
Friday 11 Dec 2020
4:34 pm

Ben Soares

JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

Options
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    • +50
    ./GPreferences.java
  2. … 1 more file in changeset.
2:33 pm

Mateusz Warowny

JAL-3690 Let's enable web services (seriously this time)

Options
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    ./GAlignFrame.java
  2. … 41 more files in changeset.
2:33 pm

Mateusz Warowny

JAL-3690 Web services and interactive workers somewhat working.

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    ./GAlignFrame.java
  2. … 41 more files in changeset.
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 13 Nov 2020
6:09 pm

Ben Soares

JAL-3775 Eclipse re-formatting commit

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    ./GPreferences.java
  2. … 5 more files in changeset.
Wednesday 19 Aug 2020
6:43 pm

Jim Procter

JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer

Options
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    • +19
    ./GAlignFrame.java
  2. … 10 more files in changeset.
6:43 pm

Jim Procter

JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties

Options
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    • +19
    ./GAlignFrame.java
  2. … 10 more files in changeset.