JAL-4418 more documentation tweaks - getting Jen Fleming's name correct

diff --git a/help/help/html/calculations/calculatedialog.png b/help/help/html/calculations/calculatedialog.png
index fdc0c0d..f772766 100644 (file)
Binary files a/help/help/html/calculations/calculatedialog.png and b/help/help/html/calculations/calculatedialog.png differ

diff --git a/help/help/html/calculations/calculations.html b/help/help/html/calculations/calculations.html
index c897cdd..422d22a 100644 (file)
--- a/help/help/html/calculations/calculations.html
+++ b/help/help/html/calculations/calculations.html
@@ -28,7 +28,7 @@
   </p>
   <img
     alt="Alignment Calculations dialog box - opened via Calculations->Tree, PCA, or PaSiMap..."
-    src="calculatedialog.png" width="350" height="241">
+    src="calculatedialog.png" width="350" height="233">
   <p>
     The <strong>Calculations Dialog</strong> (shown above) is opened via
     the <strong>Calculations&#8594;Calculate Tree, PCA or PaSiMap...</strong>

diff --git a/help/help/html/calculations/pairwise.html b/help/help/html/calculations/pairwise.html
index 1090253..04ffcb5 100755 (executable)
--- a/help/help/html/calculations/pairwise.html
+++ b/help/help/html/calculations/pairwise.html
@@ -31,7 +31,10 @@
     is not the fastest language in the world and aligning more than a
     handful of sequences will take a fair amount of time. <br> For
     each pair of sequences the best global alignment is found using
-    BLOSUM62 as the scoring matrix. The scores reported are the raw
+    BLOSUM62 as the scoring matrix. Since Jalview 2.11.4.0, the 
+    substitution matrix can be customised via the 
+    <a href="calculations.html">Calculations Dialog</a>.</p>
+  <p>The scores reported are the raw
     scores. The sequences are aligned using a dynamic programming
     technique and using the following gap penalties :
   </p>

diff --git a/help/help/html/calculations/pasimap.html b/help/help/html/calculations/pasimap.html
index e6bcbc8..15f0fb2 100755 (executable)
--- a/help/help/html/calculations/pasimap.html
+++ b/help/help/html/calculations/pasimap.html
@@ -66,7 +66,7 @@
        features lie on similar projected angles to the origin, and their distance
        only affected by 'random variation'.
   </p>
-  <p>  <img src="pasimapviewer.png" width="600px">
+  <p>  <img src="pasimapviewer.png" width="450" height="459">
   <p>
     <strong>The PaSiMap Viewer</strong>
   </p>

diff --git a/help/help/html/calculations/pasimapviewer.png b/help/help/html/calculations/pasimapviewer.png
index f40dd39..98e2326 100644 (file)
Binary files a/help/help/html/calculations/pasimapviewer.png and b/help/help/html/calculations/pasimapviewer.png differ

diff --git a/help/markdown/releases/release-2_11_4_0.md b/help/markdown/releases/release-2_11_4_0.md
index 79ab00d..47557f0 100644 (file)
--- a/help/markdown/releases/release-2_11_4_0.md
+++ b/help/markdown/releases/release-2_11_4_0.md
@@ -10,7 +10,7 @@ channel: "release"
 - <!-- JAL-4392 --> Consensus secondary structure visualization for alignments
 - <!-- JAL-4411 --> Show data source for 'reference annotation' from 3D structure (e.g. Secondary Structure)
 - <!-- JAL-4386 --> Calculate tree or PCA using secondary structure annotation
-- <!-- JAL-789,JAL-4257 --> allow adjustment of gap opening, extension, and score model for built in pairwise alignment
+<!-- not complete in this version - JAL-789,JAL-4257 -- allow adjustment of gap opening, extension, and score model for built in pairwise alignment -->
 - <!-- JAL-4447 --> Pairwise alignment can be performed with different substitution matrices
 - <!-- JAL-4447 --> PCA, Pairwise alignment, trees and PaSiMap window titles include the matrix and additional parameters used
 - <!-- JAL-4461 --> "Select format by extension" option in Jalview's "Save As" dialog's file type dropdown menu
@@ -36,27 +36,28 @@ channel: "release"
 - <!-- JAL-4454 --> "Getdown DEVELOP Channel" linkCheck fails if there's a link to whatsNew#experimental or releaseHistory from other help pages
 
 ## Issues Resolved
-- <!-- JAL-1054 -->    jalview does not fetch from a URL containing a redirect
-- <!-- JAL-4414 -->    HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
-- <!-- JAL-3409 -->    launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
-- <!-- JAL-4072 -->    Possible "Zip Slip Vulnerability" in getdown
-- <!-- JAL-4417 -->    jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties
-- <!-- JAL-4421 -->    Release installer DMG does not display the background image
-- <!-- JAL-4358 -->    Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
+- <!-- JAL-1054 --> jalview does not fetch from a URL containing a redirect
+- <!-- JAL-4414 --> HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
+- <!-- JAL-3409 --> launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
+- <!-- JAL-4072 --> Possible "Zip Slip Vulnerability" in getdown
+- <!-- JAL-4417 --> jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties
+- <!-- JAL-4421 --> Release installer DMG does not display the background image
+- <!-- JAL-4358 --> Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
 - <!-- JAL-4442 --> Race condition in Jalview quit handler that can cause a hang on very slow interactive systems
-- <!-- JAL-4460 -->    Adjusting the saved as file format via the Alignment window Save As... dialog box doesn't actually change the format used to save the alignment
+- <!-- JAL-4460 --> Adjusting the saved as file format via the Alignment window Save As... dialog box doesn't actually change the format used to save the alignment
 - <!-- JAL-4427,JAL-4451 --> Annotation labels from protein disorder services include html tags from description
 
 ### development and deployment
 
-- <!-- JAL-4111 --> removed gradle build's dependency on gradle-imagemagick plugin to allow building on windows (still need imagemagick installed on path for splashscreen commit watermark)
-- <!-- JAL-4397 -->    fixed inconsistencies in test suite on different platforms
+- <!-- JAL-4111 --> Removed gradle build's dependency on gradle-imagemagick plugin to allow building on windows (still need imagemagick installed on path for splashscreen commit watermark)
+- <!-- JAL-4397 --> Fixed inconsistencies in test suite on different platforms
 - <!-- JAL-4398 --> The rendering of the text "Window" for the Window menu item is different to the other menus when testing in Linux 
 
 
 ### New Known Issues
-- <!-- JAL-4443 -->     PaSiMap not available in JalviewJS
-- <!-- JAL-4100 -->            Jalview ignores ncrna genes when importing from genbank format files
+
+- <!-- JAL-4443 --> PaSiMap not available in JalviewJS
+- <!-- JAL-4100 -->    Jalview ignores ncrna genes when importing from genbank format files
 - <!-- JAL-4450 --> Sequence letter aspect ratio not set correctly when aspect ratio is very narrow after middle-mouse drag
 - <!-- JAL-4464 --> cannot store/restore group associated secondary structure consensus annotations
 - <!-- JAL-4349 --> spurious output image .extensions cause jalview CLI execution to fail with Null Pointer Exception (since 2.11.3.0)

diff --git a/help/markdown/whatsnew/whatsnew-2_11_4_0.md b/help/markdown/whatsnew/whatsnew-2_11_4_0.md
index 8d72ab8..2e9f15b 100644 (file)
--- a/help/markdown/whatsnew/whatsnew-2_11_4_0.md
+++ b/help/markdown/whatsnew/whatsnew-2_11_4_0.md
@@ -4,10 +4,10 @@ This release adds new capabilities for visualisation and clustering of protein s
 along with enhanced control of the display and analysis of secondary structure from different 
 sources of 3D structure and prediction. 
 
-The Calculations dialog has also been revised to accommodate a new implementation of 
-the spatial clustering method PASiMap 
+The <a href="calculations/calculations.html">Calculations dialog</a> has also been revised to accommodate a new implementation of 
+the spatial clustering method <a href="calculations/pasimap.html">PASiMap</a> 
 ([Su et al. 2022 <i>Comp. Struc. Biotech.</i>](https://doi.org/10.1016/j.csbj.2022.09.034)) 
-which was added to Jalview by Thomas Morrell and Jen Christianson.
+which was added to Jalview by Thomas Morrell and Jennifer Fleming.
 
 Jalview 2.11.4 also has new installers and command line scripts that bring several 
 minor improvements, and also makes it easier for IT admins to manage Jalview installations