From 3c74b4df923e91c55137dc1b2b5b5ce32775cdb1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 28 Feb 2022 18:57:07 +0000 Subject: [PATCH] =?utf8?q?JAL-3746=20more=20what=E2=80=99s=20new=20and=20rel?= =?utf8?q?ease=20notes?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help/help.jhm | 1 + help/help/helpTOC.xml | 9 +-- help/help/html/releases.html | 160 +++++++++++++++++++++++++++++++++++++++--- help/help/html/whatsNew.html | 2 +- 4 files changed, 157 insertions(+), 15 deletions(-) diff --git a/help/help/help.jhm b/help/help/help.jhm index 4efcd8f..78eaa70 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -150,6 +150,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 9f1942c..cbef398 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -24,9 +24,10 @@ - - - + + + + @@ -133,7 +134,7 @@ - + diff --git a/help/help/html/releases.html b/help/help/html/releases.html index a8d346b..3b74773 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -63,42 +63,182 @@ li:before {
  • + Support for viewing 3D + structures with ChimeraX and Pymol in addition to Jmol and + Chimera. +
    • +
  • + New Preferences tab for adjusting Jalview's + memory settings at launch +
    • +
  • + +
    • +
  • + +
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  • Support for Canonical Uniprot IDs
    • +
  • + Updated Jalview bindings for Uniprot XML + schema +
JalviewJS -
  • PDB structures mapped to Uniprot Sequences with SIFTS
    • -
  • +
      +
    • + PDB structures mapped to Uniprot Sequences with + SIFTS +
      • +
    • + +
      • +
    • + +
      • +
    • + +
      • +
    • + Missing message bundle keys are only + reported once per key (avoids excessive log output in js + console) +
      • +
    • + Feature type is included in the title of + the Feature Settings' Colour Chooser dialog +
      • +
    Development
      -
    • Updated building instructions
    • First integrated JalviewJS and Jalview release
      • +
    • Updated building instructions
      • +
    • + Improved JalviewJS/Jalview build process + for system package provided eclipse installs on linux +
      • +
    • Install4j 9.0.x used for installer packaging
      • +
    • Notarized MacOS installer for compatibility with Big + Sur and Monterey
      • +
    • + Uninstaller application for old + (InstallAnywhere based) Jalview installations removed from + the DMG +
      • +
    • + Improved use of installers for unattended + installation with a customizedId of "JALVIEW" in install4j's + Jalview Launcher +
      • +
      +
    • + Slow structure commands can block Jalview + execution +
      • +
    • + Structure window's viewer-specific menu + disappears when only one structure is shown (and many + sequences:one chain mappings are present) +
    • - Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3) + Annotation file: PROPERTIES apply only to + the first SEQUENCE_GROUP defined + +
      • + +
    • + Selections not + propagated between Linked CDS - Protein alignments and their + trees (known defect from 2.11.1.3)
    • Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage)
      • +
    • + X was not being recognised as the unknown base + in DNA sequences +
    • Removed RNAview checkbox and logic from Structure Preferences
      • -
    • Tooltip behaviour improved (slightly)
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    • Can edit a feature so that start > end
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    • Cancel from Amend Features doesn't reset a modified graduated colour
      • +
    • + Tooltip behaviour improved (slightly) +
      • +
    • + Can edit a feature so that start > end +
      • +
    • + Cancel from Amend Features doesn't reset a + modified graduated colour +
      • +
    • + New View with automatic 'Show Overview' + preference enabled results in Null Pointer Exceptions when + clustal colouring is enabled +
      • +
    • Can open multiple Preferences panels
      • +
    • + Standard out logging broken: messages only + routing to stderr and appear as a raw template +
      • +
    JalviewJS +
      +
    • + +
      • +
    • + +
      • +
    • + +
      • +
    • + +
      • +
    • + +
      • +
    • + JalviewJS doesn't honour arguments passed + via Info.args when there are arguments on the URL +
      • +
    • + gradle closure-compiler not using UTF-8 +
      • +
    • + Annotation file fails to load from URL in + JalviewJS +
    Development
      -
    • Gradle
      • Fixed non-fatal gradle errors during build
        • -
      • Updated build.gradle for use with Gradle v.6.6+
      • - +
    • Gradle +
        +
      • Fixed non-fatal gradle errors during build
        • +
      • + Updated build.gradle for use with + Gradle v.6.6+ +
        • +
      +
      • +
    diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 5ecf293..9ee2ab0 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -38,7 +38,7 @@
    • Linked viewing with ChimeraX and - PyMol
      Simply configure your prefered viewer for 3D + PyMol
      Simply configure your preferred viewer for 3D molecular data in Jalview's structure preferences, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure -- 1.7.10.2