From fbc163d1dfc48187b15af561d07b1c62778920d1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 28 Feb 2022 18:30:02 +0000 Subject: [PATCH] JAL-3503 2.11.2.0 release notes and docs --- help/help/help.jhm | 1 + help/help/html/features/preferences.html | 15 ++++++++ help/help/html/memory.html | 56 ++++++++++++++++++------------ help/help/html/whatsNew.html | 1 + 4 files changed, 51 insertions(+), 22 deletions(-) diff --git a/help/help/help.jhm b/help/help/help.jhm index 449f34c..4efcd8f 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -60,6 +60,7 @@ + diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html index 5a3fe7a..d091272 100755 --- a/help/help/html/features/preferences.html +++ b/help/help/html/features/preferences.html @@ -64,6 +64,10 @@
  • The "Editing" Preferences tab contains settings affecting behaviour when editing alignments.
    • +
  • The "Startup" + Preferences tab allows you to adjust how much memory is + allocated to Jalview when it is launched. +
  • The "Web Service" Preferences tab allows you to configure the JABAWS @@ -419,6 +423,17 @@ loaded onto the alignment will automatically sort the alignment.

     

    +

    + Startup +

    +

    + When Jalview is launched it by default examines the available memory + and requests up to 90% to be allocated to the application, or 32G, + which ever is smaller. The Startup tab allows you to adjust + the maximum percentage and hard limits for Jalview memory allocation + stored in your .jalview_properties file. +

    +

     

    Web Services Preferences - documentation for this tab is given in the Web Services diff --git a/help/help/html/memory.html b/help/help/html/memory.html index 7d6fb85..ec57530 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -30,9 +30,13 @@

    When launched as an Application, Jalview will automatically configure the amount of memory allocated to the program to be 90% of - physical memory. You may wish to change this behaviour - - particularly if you are working on a machine that runs other memory - intensive processes. + physical memory, or 32GB - which ever is smaller.

    +

    + This behaviour might not be ideal if you are working on a machine + that runs other memory intensive processes, and (since + Jalview 2.11.2) can be changed via the Startup Preferences panel. +

    Signs that Jalview is Running out of Memory
    If Jalview has not explicitly told you that it has run out of memory, @@ -65,28 +69,36 @@

      -
    • JVL file
      The easiest - way to launch Jalview with a different percentage of physical - memory available is to create a text file with extension .jvl +
    • Jalview's Startup + Preferences panel
      The easiest way to launch Jalview + with a different percentage of physical memory available is to + adjust your user preferences via the Startup Preferences panel.
      • +
    • JVL file
      Another way + to adjust launch settings is with a text file with extension .jvl and a single line to specify the percentage of memory you wish Jalview to request: 
      -      jalview.jvmmempc=50
      In Windows and in macOS you can then launch Jalview by - double clicking on this file, and your memory setting will be used - instead of the default value.

      In Linux or other - unix variants you can launch Jalview on the command line and - provide your JVL file as an argument with 
      -      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
      If you want to use a memory setting like this and open a - file you can use both the jvl and alignment files as command line - arguments, but you must put the jvl file first, e.g. 
      -      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
      Alternatively, you can use the standard Jalview command line + jalview.jvmmempc=50 In Windows and in macOS you can then launch + Jalview by double clicking on this file, and your memory setting + will be used instead of the default value.

      In + Linux or other unix variants you can launch Jalview on the command + line and provide your JVL file as an argument with 
      +      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
      If you + want to use a memory setting like this and open a file you can use + both the jvl and alignment files as command line arguments, but + you must put the jvl file first, e.g. 
      +      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
      + Alternatively, you can use the standard Jalview command line arguments with or without the jvl file (first), e.g. 
      -       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
      You can use command line arguments to control memory - settings in Windows and macOS too:
      In Windows you must - use, e.g. 
      -      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
      In macOS you can use the macOS open command like this: 
      -      open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa
      (put all the Jalview arguments after the --args - parameter) -

      • + /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal + You can use command line arguments to control memory settings in + Windows and macOS too:
      In Windows you must use, e.g. 
      +      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
      + In macOS you can use the macOS open command like this: 
      +      open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa
      (put + all the Jalview arguments after the --args parameter) +
      +
    • Maximum memory limit
      Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit': 
      jalview.jvmmemmax = 32G
      diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index f529c56..5ecf293 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -50,6 +50,7 @@ allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources.
      • +
    • Easier configuration of Jalview's memory allocation

      Retrieval of 3D models via 3D-Beacons
      The 3D-Beacons network (