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 (file)
--- 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"
 - <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
 - <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS  based on Chromium for Tests (still work in progress)
 
+
 ## Issues Resolved
 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
 - <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
@@ -110,13 +111,14 @@ channel: "release"
 - <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
 - <!-- JAL-3921 --> 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
 - <!-- JAL-4303 --> 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.
 - <!-- JAL-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
 - <!-- JAL-4338 --> PAE partition not shown in the same place when tree is closed and reopened
 - <!-- 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-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0
+- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
 - <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
 - <!-- 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
@@ -124,7 +126,7 @@ channel: "release"
 - <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
 - <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
 - <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
-- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window)
+- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window
 - <!-- JAL-4157 --> Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
 - <!-- JAL-4327 --> When the Groovy console is open Jalview does not prompt to save before quitting  
 - <!-- JAL-4328 --> 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 (executable)
--- 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,