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Thursday 25 Mar
7:27 pm

Ben Soares

JAL-3633 refactored/simplified LaunchUtils code

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    ./data/Application.java
  2. … 8 more files in changeset.
Friday 19 Mar
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.

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    ./data/Application.java
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Thursday 11 Mar
5:12 pm

Ben Soares

JAL-3523 Remove getdown setting the working directory to appdir

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    ./data/Application.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
Tuesday 15 Sep 2020
4:08 pm

Ben Soares

JAL-3718 fixed getdown auto-update for future updates. Getdown src files only

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    ./data/Application.java
  2. … 1 more file in changeset.
Monday 14 Sep 2020
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

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    ./data/Application.java
  2. … 5 more files in changeset.
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

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    ./data/Application.java
  2. … 5 more files in changeset.
Wednesday 19 Aug 2020
12:38 am

Ben Soares

JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.

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    ./data/Application.java
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    ./tools/Digester.java
  3. … 18 more files in changeset.
Thursday 09 Jul 2020
3:57 pm

Ben Soares

JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview

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    ./data/Application.java
  2. … 1 more file in changeset.
3:57 pm

Ben Soares

JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview

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    ./data/Application.java
Friday 15 May 2020
9:04 pm

Ben Soares

JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher

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    ./data/Application.java
  2. … 16 more files in changeset.
9:04 pm

Ben Soares

JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher

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    ./data/Application.java
  2. … 16 more files in changeset.
Wednesday 19 Feb 2020
3:22 pm

Jim Procter

(Notes for self) - Ben verified on linux, OSX, Windows. Need to check there are docs and logging to indicate that the hard limit is reached, so if people want to adjust the limit they can !

(Notes for self) - Ben verified on linux, OSX, Windows.
Need to check there are docs and logging to indicate that the hard limit is reached, so if people want to adjust the limit they can !

3:20 pm

Jim Procter

JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute...
JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute...
3:19 pm

Jim Procter

Monday 17 Feb 2020
2:49 pm

Ben Soares

JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mentioning common-compress updated.

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    ./data/Application.java
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    ./data/Resource.java
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    ./util/FileUtil.java
  4. … 16 more files in changeset.
Thursday 09 Jan 2020
4:29 pm

Ben Soares

Changing "... 8GB ..." to "... " + (noMemMaxHeapSizeDefault + 536870912) / 1073741824 + "GB ..." which does the trick! This should turn out to be the nearest integer number of GB being set (calcula...

Changing
"... 8GB ..."
to
"... " + (noMemMaxHeapSizeDefault + 536870912) / 1073741824 + "GB ..."
which does the trick!
This should turn out to be the nearest integer number of GB being set (calculated as (long)((mem+0.5GB)/1GB) ).

Just got to the comment about setting constant GIGABYTE. That makes much more sense and is much more readable

Wednesday 08 Jan 2020
4:45 pm

Ben Soares

I agree the getdown (adapted) source that we use is not in the right place. Currently all getdown resources and built components get put under ./getdown/ to keep it a separate entity from Jalview. ...

I agree the getdown (adapted) source that we use is not in the right place. Currently all getdown resources and built components get put under ./getdown/ to keep it a separate entity from Jalview. I've created an issue detailing where the different getdown folders should be moved to (including putting ./getdown/src under ./src), but the build process for getdown is still necessarily separate from the Jalview build process. See issue JAL-3500.

Monday 30 Dec 2019
1:55 am

Ben Soares

JAL-3394 catch a null pointer exception, when URI not parsed but not malformed ???

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    ./data/Application.java
  2. … 5 more files in changeset.
Friday 20 Dec 2019
2:35 pm

Mungo Carstairs

A public class with no public members doesn't quite make sense. Should maybe have default (package) visiblity (or be an inner class of MemorySetting)? In fact, can't this just be another method in ...

A public class with no public members doesn't quite make sense. Should maybe have default (package) visiblity (or be an inner class of MemorySetting)?
In fact, can't this just be another method in MemorySetting?

2:31 pm

Mungo Carstairs

Method javadoc please?

Method javadoc please?

1:45 pm

Mungo Carstairs

Should the getdown code be in a jar file? And include MemorySettings? cf comment https://issues.jalview.org/browse/?focusedCommentId=21949&page=com.atlassian.jira.plugin.system.issuetabpanels:comme...

Should the getdown code be in a jar file? And include MemorySettings?
cf comment https://issues.jalview.org/browse/?focusedCommentId=21949&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3278comment-21949

Not having getdown/data/Application on the project classpath confused me a bit (calls from Application to MemorySettings don't show up).

1:43 pm

Mungo Carstairs

do this in getMemorySetting() instead ...cancel that...I see this is called from getdown/data/Application and either or both property might be null.

do this in getMemorySetting() instead
...cancel that...I see this is called from getdown/data/Application and either or both property might be null.

12:06 pm

Mungo Carstairs

Declare type as List<String> is preferred style (refer to types by their interfaces wherever possible)

Declare type as List<String> is preferred style (refer to types by their interfaces wherever possible)

12:05 pm

Mungo Carstairs

Compiler warning: loop label ARG is never referenced

Compiler warning: loop label ARG is never referenced

12:04 pm

Mungo Carstairs

Needs class and main method Javadoc

Needs class and main method Javadoc