From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 26 May 2017 16:37:31 +0000 (+0100)
Subject: JAL-2418 updated JPred documentation and screenshot for JPred4
X-Git-Tag: Release_2_10_2~3^2~69^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=57db03ae9b6b80c19901d604b376b41f6fbab31a;p=jalview.git

JAL-2418 updated JPred documentation and screenshot for JPred4
---

diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 077ace6..e42a4e6 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -96,9 +96,14 @@
     <li>Lupas_21, Lupas_14, Lupas_28<br> <em>Coiled-coil
         predictions for the sequence. These are binary predictions for
         each location.</em></li>
-    <li>JNETSOL25,JNETSOL5,JNETSOL0<br> <em>Solvent
-        accessibility predictions - binary predictions of 25%, 5% or 0%
-        solvent accessibility.</em></li>
+    <li>Jnet Burial<br> <em>Prediction of Solvent
+        Accessibility. levels are
+        <ul>
+          <li>0 - Exposed</li>
+          <li>3 - 25% or more S.A. accessible</li>
+          <li>6 - 5% or more S.A. accessible</li>
+          <li>9 - Buried (<5% exposed)</li>
+        </ul></li>
     <li>JNetPRED<br> <em>The consensus prediction -
         helices are marked as red tubes, and sheets as dark green
         arrows.</em></li>
@@ -112,13 +117,8 @@
     <li>JNetHMM<br> <em>HMM profile based prediction -
         helices are marked as red tubes, and sheets as dark green
         arrows.</em></li>
-    <li>jpred<br> <em>Jpred prediction - helices are
-        marked as red tubes, and sheets as dark green arrows.</em></li>
     <li>JNETPSSM<br> <em>PSSM based prediction - helices
         are marked as red tubes, and sheets as dark green arrows.</em></li>
-    <li>JNETFREQ<br> <em>Amino Acid frequency based
-        prediction - helices are marked as red tubes, and sheets as dark
-        green arrows.</em></li>
     <li>JNETJURY<br> <em>A '*' in this annotation
         indicates that the JNETJURY was invoked to rationalise
         significantly different primary predictions.</em></li>
@@ -129,8 +129,8 @@
     href="../features/annotation.html#seqannots">Add reference
       annotation</a> Sequence ID popup menu option.
   </em>
-  <em>As of Jalview 2.6, the JPred service accessed accessed via the
-    'Secondary structure prediction' submenu should be considered a
+  <em>As of Jalview 2.6, the JPred service accessed accessed via
+    the 'Secondary structure prediction' submenu should be considered a
     legacy Jalview SOAP service, and will be replaced in the near future
     by a JPred4 Rest service.</em>
 
diff --git a/help/html/webServices/jnetprediction.gif b/help/html/webServices/jnetprediction.gif
old mode 100755
new mode 100644
index 3f827d9..006c50d
Binary files a/help/html/webServices/jnetprediction.gif and b/help/html/webServices/jnetprediction.gif differ