From 2f0ae5beea0efcf3c40a7ebec33217ac34f90320 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Mon, 9 May 2022 22:58:46 +0100 Subject: [PATCH] JAL-4004 remove stray empty h3 headers --- help/markdown/releases/release-2_10_2b1.md | 2 -- help/markdown/releases/release-2_10_3.md | 1 - help/markdown/releases/release-2_10_4.md | 1 - help/markdown/releases/release-2_10_4b1.md | 2 -- help/markdown/releases/release-2_10_5.md | 2 -- help/markdown/releases/temp | 41 ++++++++++++++++++++++++++++ 6 files changed, 41 insertions(+), 8 deletions(-) create mode 100644 help/markdown/releases/temp diff --git a/help/markdown/releases/release-2_10_2b1.md b/help/markdown/releases/release-2_10_2b1.md index d066724..e659bfc 100644 --- a/help/markdown/releases/release-2_10_2b1.md +++ b/help/markdown/releases/release-2_10_2b1.md @@ -8,7 +8,6 @@ date: 2017-09-07 -### - Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white) - Overview tab in Jalview Desktop Preferences - Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated @@ -18,7 +17,6 @@ date: 2017-09-07 -### - Overview window redraws every hidden column region row by row - duplicate protein sequences shown after retrieving Ensembl crossrefs for sequences from Uniprot - Overview window throws NPE if show boxes format setting is unticked diff --git a/help/markdown/releases/release-2_10_3.md b/help/markdown/releases/release-2_10_3.md index 64b1f95..c3ba109 100644 --- a/help/markdown/releases/release-2_10_3.md +++ b/help/markdown/releases/release-2_10_3.md @@ -8,7 +8,6 @@ date: 2017-11-17 -### - Faster and more efficient management and rendering of sequence features - More reliable Ensembl fetching with HTTP 429 rate limit request hander - Structure views don't get updated unless their colours have changed diff --git a/help/markdown/releases/release-2_10_4.md b/help/markdown/releases/release-2_10_4.md index ad0c592..0c0aff8 100644 --- a/help/markdown/releases/release-2_10_4.md +++ b/help/markdown/releases/release-2_10_4.md @@ -8,7 +8,6 @@ date: 2018-05-10 -### - New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views - Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them. - Jalview uses HTTPS for Uniprot, Xfam and Ensembl services diff --git a/help/markdown/releases/release-2_10_4b1.md b/help/markdown/releases/release-2_10_4b1.md index 824a70a..e4a463b 100644 --- a/help/markdown/releases/release-2_10_4b1.md +++ b/help/markdown/releases/release-2_10_4b1.md @@ -8,7 +8,6 @@ date: 2018-06-07 -### - Use HGVS nomenclature for variant annotation retrieved from Uniprot - Windows File Shortcuts can be dragged onto the Jalview Desktop @@ -17,7 +16,6 @@ date: 2018-06-07 -### - Cannot import features with multiple variant elements (blocks import of some Uniprot records) - Clustal files with sequence positions in right-hand column parsed correctly - Wrap view - export to SVG - IDs shown but not alignment area in exported graphic diff --git a/help/markdown/releases/release-2_10_5.md b/help/markdown/releases/release-2_10_5.md index 45133bd..52487e0 100644 --- a/help/markdown/releases/release-2_10_5.md +++ b/help/markdown/releases/release-2_10_5.md @@ -8,7 +8,6 @@ date: 2018-09-10 -### - Default memory for Jalview webstart and InstallAnywhere increased to 1G. - Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. *Display is configured via the Format menu, or for command-line use via a Jalview properties file.* - Ensembl client updated to Version 7 REST API and sequence data now imported as JSON. @@ -23,7 +22,6 @@ date: 2018-09-10 -### - Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment. - Annotation obscures sequences if lots of annotation displayed. - Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected diff --git a/help/markdown/releases/temp b/help/markdown/releases/temp new file mode 100644 index 0000000..52487e0 --- /dev/null +++ b/help/markdown/releases/temp @@ -0,0 +1,41 @@ +--- +channel: release +version: 2.10.5 +date: 2018-09-10 +--- + +## New Features + + + + - Default memory for Jalview webstart and InstallAnywhere increased to 1G. + - Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. *Display is configured via the Format menu, or for command-line use via a Jalview properties file.* + - Ensembl client updated to Version 7 REST API and sequence data now imported as JSON. + - Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property. + + +### Development + - Support added to execute test suite instrumented with [Open Clover](http://openclover.org/) + + +## Issues Resolved + + + + - Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment. + - Annotation obscures sequences if lots of annotation displayed. + - Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected + - Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible. + - Alignment is black in exported EPS file when sequences are selected in exported view. + - Groups with different coloured borders aren't rendered with correct colour. + - Jalview could hang when importing certain types of knotted RNA secondary structure. + - Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1. + - '.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile. + - Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure. + - .jvp should be used as default extension (not .jar) when saving a Jalview project file. + - Mac Users: closing a window correctly transfers focus to previous window on OSX + + +### Java 10 Issues Resolved + - OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box. + - Jalview now uses patched version of the [VAqua5](https://violetlib.org/vaqua/overview.html) 'look and feel' which has improved compatibility with the latest version of OSX. -- 1.7.10.2