From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 10 Sep 2015 02:10:58 +0000 (+0100)
Subject: JAL-1645 links from whats New page
X-Git-Tag: Release_2_10_0~442
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a5a0d509e08a0b6db7fd92a14006b7a3f2be22cf;hp=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;p=jalview.git

JAL-1645 links from whats New page
---

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index e7017f0..e9f8e8f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -173,7 +173,7 @@
 				href="../features/varna.html">VARNA</a>.
 		</em>
 		</li>
-    <li><strong>Hide Insertions</strong><br />
+    <li><a name="hideinserts"/><strong>Hide Insertions</strong><br />
     <em>Hides columns containing gaps in the current sequence or
         selected region, and reveals columns not including gaps.</em>
     <li><strong>Hide Sequences</strong><br> <em>Hides the
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index b115385..693b0f0 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -45,8 +45,8 @@
       reconstructed from protein alignments calculated by Jalview's web
       services, and update in response to edits in the amino acid view.<br />To
       start experimenting with cDNA/Protein analysis, jut drop a file
-      containing cDNA sequences which code for, and have IDs matching
-      proteins in an existing alignment, and Jalview will do the rest.</li>
+      containing cDNA sequences which code for proteins in an existing
+      alignment, and Jalview will do the rest.</li>
     <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
       2.9 provides full support for the use of Chimera to view 3D
       structures linked to alignment views in the Jalview Desktop. We've
@@ -58,7 +58,7 @@
       much more responsive, and selected regions in Chimera are now
       shown as highlighted regions in the Jalview desktop.</li>
     <li><strong>Interactive querying of the PDBe</strong><br />Jalview
-      users can now browse and retrieve 3D structure data from the PDB
+      users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
       via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
         Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
         et al 2014</a>). Developed in collaboration with the PDBe group at
@@ -74,12 +74,13 @@
       including the loss of pseudoknots when RNA secondary structure is
       shown VARNA.</li>
     <li><strong>Protein Secondary Structure predictions
-        with JPred4</strong><br/>Jalview includes a number of new features for working
-      with secondary structure predictions from the JPred4 server. These
-      include the ability to automatically hide insertions and highlight
-      mutations in an alignment with respect to a reference sequence.
-      Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable SVG HTML export</a> was also
-      developed specifically for the JPred4 server.</li>
+        with JPred4</strong><br />Jalview includes a number of new features for
+      working with secondary structure predictions from the JPred4
+      server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
+      mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
+        Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
+        SVG HTML export</a> was also developed specifically for the JPred4
+      server.</li>
   </ul>
 
 </body>