From: James Procter Date: Wed, 15 Nov 2023 16:09:35 +0000 (+0000) Subject: Merge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop X-Git-Tag: Release_2_11_3_0^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=34538821944021020be4bc7923414fd1d2021a1c;hp=0b2df62f9d5ffe2b2fbfd3652a257f4234a9bf9f;p=jalview.git Merge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop --- diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 5299026..47b3778 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -78,6 +78,7 @@ channel: "release" - Output stderr and stdout when running tests via gradle - New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress) + ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - Unsaved Alignment windows close without prompting to save, individually or at application quit. @@ -110,13 +111,14 @@ channel: "release" - Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies - Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x) -## New Known defects + +### New Known Issues - EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu. - Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled. - PAE partition not shown in the same place when tree is closed and reopened - Cannot cancel structure view open action once it has been started via the structure chooser dialog - Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately -- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0 +- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0) - Overview shown and then closed when importing legacy jalview projects without overview store/restore information - Missing last letter when copying consensus sequence from alignment if first column is hidden - Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export @@ -124,7 +126,7 @@ channel: "release" - Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation - scripts adding new fileformats or colourschemes do not work when run via command line - Headless alignment export with structure annotations doesn't include secondary structure and temperature factor -- Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window) +- Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window - Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu - When the Groovy console is open Jalview does not prompt to save before quitting - Jalview works with but is not fully compatible with latest Ensembl REST API (15.6) diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 3ee3316..76020c7 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -398,13 +398,13 @@ public class IdCanvas extends JPanel implements ViewportListenerI * * @param g * @param av2 - * @param i + * @param startSeq * @param totalHeight */ - public void drawIdsWrappedNoGUI(Graphics2D g, AlignViewport av2, int i, - int totalHeight) + public void drawIdsWrappedNoGUI(Graphics2D g, AlignViewport av2, + int startSeq, int totalHeight) { - drawIdsWrapped(g, av2, totalHeight, totalHeight, i, false); + drawIdsWrapped(g, av2, startSeq, totalHeight, -1, false); } public void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,