From 4fbf1d10221c2780c3ec9c8f9cc080ffae392c61 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 7 Sep 2023 16:28:46 +0100 Subject: [PATCH] JAL-4279 move on if the file doesn't exist, or Identify fails for the file. --- help/markdown/releases/release-2_11_3_0.md | 10 +++++++++- src/jalview/bin/Commands.java | 2 ++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 2365cf3..087993c 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -8,7 +8,7 @@ channel: "release" - Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 - Installers built with install4j10 - Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button -- FlatLAF default look and feel on Linux, OSX and everywhere else ? +- FlatLAF default look and feel on Linux, OSX and everywhere else - Ambiguous Base Colourscheme - Find can search sequence features' type and description @@ -71,6 +71,8 @@ known issue ? 'Reload' for a jalview project results in all wi - Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - In Linux desktops' task-managers, the grouped Jalview windows get a generic name +- Improved file chooser's 'recent files' view and added filter for 'All known alignment files' +- Relative files added to recent files list via import from command line are selected when Jalview opened from same location ## Still in progress (delete on release) @@ -81,9 +83,11 @@ known issue ? 'Reload' for a jalview project results in all wi ### Development and Deployment - Create separate gradle test task for some tests +- Prevent gradle test on macOS continuously grabbing focus - Allow gradle build to create suffixed DEVELOP-... builds with channel appbase - Jalview bio.tools description maintained under jalview's git repo and bundled with source release + ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - Cancelling interactive calculation leaves empty progress bar. @@ -103,12 +107,16 @@ known issue ? 'Reload' for a jalview project results in all wi - Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window - Overview window is saved in project file, and state of 'show hidden regions' is preserved. - JvCacheableInputBoxTest flaky on build server +- SLF4J produces an error to STDERR at Jalview startup due to missing class +- 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 - 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 +- Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x) + diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 9cacc83..8164182 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -217,6 +217,7 @@ public class Commands if (!(new File(openFile)).exists()) { Console.warn("Can't find file '" + openFile + "'"); + continue; } } } @@ -231,6 +232,7 @@ public class Commands } catch (FileFormatException e1) { Console.error("Unknown file format for '" + openFile + "'"); + continue; } af = afMap.get(id); -- 1.7.10.2