From 0c1ab6aa5767dc2ff0f40f694af9b0181148b1f5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 15 Sep 2021 16:00:20 +0100 Subject: [PATCH] JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax --- help/help/html/features/clarguments.html | 11 ++++++- help/help/html/features/commandline.html | 27 ++++++++++++++-- help/help/html/releases.html | 51 +++++++++++++++++++++++++++++- 3 files changed, 84 insertions(+), 5 deletions(-) diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index 0d800cf..1eecfb9 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -34,6 +34,11 @@ parameters, then include it at the beginning of the command line to ensure they are processed before any remaining arguments.
+ Typical command line execution follows the following pattern: + 
+  jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+
+ @@ -41,7 +46,11 @@ User Interface. (automatically disables questionnaire, version and usage stats checks) - + + + + -- 1.7.10.2
-nodisplay
-open FILE/URL
Specify the alignment file to + open or process by providing additional arguments.
-props FILE/URL
Use the given Jalview properties diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index e00d390..f0e04d5 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -65,10 +65,31 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa(put

Passing JVM Arguments to Jalview
If you need - to modify parameters for Jalview's Java Virtual Machine, then take a - look at the instructions for how to setting - the JVM's maximum memory. + to modify parameters for Jalview's Java Virtual Machine, or + configure system properties, then take a look at the instructions + for how to setting the JVM's + maximum memory.
+

+ Changing Jalview's 'Look and Feel'
If you + are experiencing issues with the font size or layout of Jalview's + GUI, you can try changing Jalview's 'Look and feel' by + specifying a custom system property 'laf' on startup (see setting the JVM's memory for + instructions on how to do this for your platform).
For the + Jalview standalone executable jar, simply provide one of the + property settings before the -jar argument

+
    +
  • -Dlaf=system (default look and feel for the OS)
    • +
  • -Dlaf=crossplatform (Java's Metal Look and Feel)
    • +
  • -Dlaf=nimbus (Java's alternative Nimbus Look and Feel)
    • +
  • -Dlaf=mac (only has an effect on OSX)
    • +
  • -Dlaf=gtk (only has an effect on Linux)
    • +
+ The currently configured look and feel is logged to Jalview's console. + Once the look and feel has been changed, it will be stored in + Jalview's .jalview_properties file for future Jalview sessions. +

 

 

diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 83a9cc3..6820883 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -66,7 +66,37 @@ li:before { Shift+arrow keys navigate to next gap or residue in cursor mode -
  • +
  • + Support import of VCF 4.3 by updating + HTSJDK from 2.12 to 2.23 +
    • +
  • + IntervalStore library updated to v.1.1: + optimisations and improvements suggested by Bob Hanson and + improved compatibility with JalviewJS +
    • +
  • + Retrieve GZipped stockholm formatted + alignments from Pfam and Rfam +
    • +
  • + Recognise GZipped content for URLs and File + import (no longer based on .gz extension) +
    • +
  • + Updated Spanish Translation for 2.11.1 +
    • +
  • + Migrate EMBL record retrieval to use latest + ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and + EMBL flat file +
    • + Launching Jalview +
      +
    • + Configure Jalview Desktop's look and feel + through a system property +
    		@@ -83,6 +113,25 @@ li:before { Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig +
  • + Errors encountered when processing variants + from VCF files yield "Error processing VCF: Format specifier + '%s'" on the console +
    • +
  • + Count of features not shown can be wrong + when there are both local and complementary features mapped + to the position under the cursor +
    • +
  • + Slider with negative range values not + rendered correctly in VAqua4 (Since 2.10.4) +
    • + + New Known defects +
      +
    • Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch) +