JAL-2975,JAL-2647,JAL-1767,JAL-2965, JAL-3111 updated PCA viewer documentation

diff --git a/help/help/html/calculations/pca.html b/help/help/html/calculations/pca.html
index 3529cae..3bf21cb 100755 (executable)
--- a/help/help/html/calculations/pca.html
+++ b/help/help/html/calculations/pca.html
@@ -70,7 +70,7 @@
       nucleotide substitution matrix</a>, or by sequence percentage identity,
       or sequence feature similarity. 
   </p>
       nucleotide substitution matrix</a>, or by sequence percentage identity,
       or sequence feature similarity. 
   </p>

-  <img src="pcaviewer.gif">
+  <img src="pcaviewer.png">

   <p>
     <strong>The PCA Viewer</strong>
   </p>
   <p>
     <strong>The PCA Viewer</strong>
   </p>

@@ -84,7 +84,9 @@
     towards the front of the view.</p>
   <p>
     The 3d view can be rotated by dragging the mouse with the <strong>left
     towards the front of the view.</p>
   <p>
     The 3d view can be rotated by dragging the mouse with the <strong>left

-      mouse button</strong> pressed. The view can also be zoomed in and out with
+      mouse button</strong> pressed, or with the <strong>arrow
+      keys</strong> when <strong>SHIFT</strong> is pressed. The
+    view can also be zoomed in and out with

     the up and down <strong>arrow keys</strong> (and the roll bar of the
     mouse if present). Labels will be shown for each sequence if the
     entry in the View menu is checked, and the plot background colour
     the up and down <strong>arrow keys</strong> (and the roll bar of the
     mouse if present). Labels will be shown for each sequence if the
     entry in the View menu is checked, and the plot background colour

@@ -122,7 +124,7 @@ left-clicking and dragging the mouse over the display. -->
   <p>
     Initially, the display shows the first three components of the
     similarity space, but any eigenvector can be used by changing the
   <p>
     Initially, the display shows the first three components of the
     similarity space, but any eigenvector can be used by changing the

-    selected dimension for the x, y, or z axis through each ones menu
+    selected dimension for the x, y, or z axis through each one's menu

     located below the 3d display. The <strong><em>Reset</em></strong>
     button will reset axis and rotation settings to their defaults.
   </p>
     located below the 3d display. The <strong><em>Reset</em></strong>
     button will reset axis and rotation settings to their defaults.
   </p>

@@ -131,7 +133,7 @@ left-clicking and dragging the mouse over the display. -->
     <em>The output of points and transformed point coordinates was
       added to the Jalview desktop in v2.7.</em> <em>The Reset button
       and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
     <em>The output of points and transformed point coordinates was
       added to the Jalview desktop in v2.7.</em> <em>The Reset button
       and Change Parameters menu were added in Jalview 2.8.</em> <em>Support

-      for PAM250 based PCA was added in Jalview 2.8.1.</em>
+      for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em> 

   </p>
   <p>
     <strong>Reproducing PCA calculations performed with older
   </p>
   <p>
     <strong>Reproducing PCA calculations performed with older

diff --git a/help/help/html/calculations/pcaviewer.gif b/help/help/html/calculations/pcaviewer.gif
deleted file mode 100644 (file)
index 78c82f2..0000000
Binary files a/help/help/html/calculations/pcaviewer.gif and /dev/null differ

diff --git a/help/help/html/calculations/pcaviewer.png b/help/help/html/calculations/pcaviewer.png
new file mode 100644 (file)
index 0000000..7dc5b80
Binary files /dev/null and b/help/help/html/calculations/pcaviewer.png differ