From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 7 Sep 2023 15:28:46 +0000 (+0100)
Subject: JAL-4279 move on if the file doesn't exist, or Identify fails for the file.
X-Git-Tag: Release_2_11_4_0~183
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4fbf1d10221c2780c3ec9c8f9cc080ffae392c61;p=jalview.git

JAL-4279 move on if the file doesn't exist, or Identify fails for the file.
---

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"
 - <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
 - <!-- JAL-4054 --> Installers built with install4j10
 - <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
-- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else ?
+- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else
 
 - <!-- JAL-4019 --> Ambiguous Base Colourscheme
 - <!-- JAL-4061 --> Find can search sequence features' type and description
@@ -71,6 +71,8 @@ known issue ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 
 - <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
 - <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
+- <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
+- <!-- JAL-4206 --> 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 ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 ### Development and Deployment
 
 - <!-- JAL-4167 --> Create separate gradle test task for some tests
+- <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
 - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
 - <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
 
+
 ## Issues Resolved
 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
 - <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
@@ -103,12 +107,16 @@ known issue ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 - <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
 - <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
 - <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
+- <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
+- <!-- 
 
 ## New Known defects
 - <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
 - <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
 - <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
+- <!-- JAL-3024 --> 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);