From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 17 Jun 2019 12:46:28 +0000 (+0100)
Subject: JAL-2975,JAL-2647,JAL-1767,JAL-2965, JAL-3111 updated PCA viewer documentation
X-Git-Tag: Release_2_11_0~7^2~4^2^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e185cfd4324bf9e2277e25cfc280cc8a23e75360;p=jalview.git

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
--- 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>
-  <img src="pcaviewer.gif">
+  <img src="pcaviewer.png">
   <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
-      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
@@ -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
-    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>
@@ -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
-      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
diff --git a/help/help/html/calculations/pcaviewer.gif b/help/help/html/calculations/pcaviewer.gif
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diff --git a/help/help/html/calculations/pcaviewer.png b/help/help/html/calculations/pcaviewer.png
new file mode 100644
index 0000000..7dc5b80
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