From 1098b4a552de1dc8ada14f6a9354c9d80e6721a0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 13 Nov 2017 13:00:17 +0000
Subject: [PATCH] JAL-2810 updated help docs for auto search checkbox and
 retrieve IDs tab

---
 help/html/features/pdbsequencefetcher.html     |   24 ++++++++++++++----------
 help/html/features/uniprotsequencefetcher.html |   18 +++++++++---------
 2 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html
index 2962ba6..bb63bed 100644
--- a/help/html/features/pdbsequencefetcher.html
+++ b/help/html/features/pdbsequencefetcher.html
@@ -37,7 +37,7 @@
   <p>
     To open the PDB Sequence Fetcher, select PDB as the database from
     any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
-    <strong>&quot;File &#8594;Fetch Sequences&quot;</strong>).
+    <strong>&quot;File &#8594;Fetch Sequences&quot;</strong>). 
   </p>
   <img src="pdbseqfetcher.png" align="left"
     alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
@@ -45,13 +45,18 @@
   <p>
     <strong>Searching the PDB Database</strong>
   </p>
+  <p>To search the PDB, begin typing in the text box. If the
+    'autosearch' checkbox is enabled, then the results of your query
+    will be automatically updated and shown in the search results tab;
+    otherwise, press return to update the results. To access previous
+    searches, press the down-arrow or click the drop down menu icon at
+    the side of the search box. If you just want to paste in a list of
+    IDs, the 'Retrieve IDs' tab provides a batch-retrieval interface.</p>
   <p>
-    To search the PDB, begin typing in the text box. The results of your
-    query are shown in the search results tab, which updates every time
-    you type in the search text box. You can sort results according to
-    the displayed columns, and select entries with the mouse and
-    keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
-    button to retrieve and view them in Jalview.
+    You can sort results according to the displayed columns, and select
+    entries with the mouse and keyboard. Once you have selected one or
+    more entries, hit the <strong>OK</strong> button to retrieve and
+    view them in Jalview.
   </p>
   <p>
   <ul>
@@ -64,9 +69,8 @@
       1xyz:A</li>
 
     <li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
-      IDs can be specified by separating them with a semi-colon.<br />
-      e.g. 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically
-      fetch those IDs, like the default Sequence Fetcher interface.</li>
+      IDs can be specified for retrieval via the 
+      <strong>Retrieve IDs</strong> tab.</li>
 
     <li><strong>Wild card searching</strong><br>The following
       wild cards are supported by the EMBL-EBI PDBe query service:
diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html
index edd8995..4a64f52 100644
--- a/help/html/features/uniprotsequencefetcher.html
+++ b/help/html/features/uniprotsequencefetcher.html
@@ -46,10 +46,13 @@
   <p>
     <strong>Searching the UniProt Database</strong>
   </p>
-  <p>
-    To search UniProt, simply begin typing in the text box. After a
-    short delay (about 1.5 seconds), results will be shown in the table
-    below. You can sort results by clicking on the displayed columns,
+  <p>To search UniProt, simply begin typing in the text box. If the
+    'autosearch' check box is enabled, then after a short delay (about
+    1.5 seconds), results will be shown in the table below. Results are
+    also updated whenever you press Enter, and you can access previous
+    searches by pressing the 'Down' arrow or clicking the drop-down menu
+    icon at the side of the search box.</p>
+  <p>You can sort results by clicking on the displayed columns,
     and select entries with the mouse or keyboard. Once you have
     selected one or more entries, hit the <strong>OK</strong> button to
     retrieve the sequences.
@@ -61,11 +64,8 @@
 
 
     <li><strong>Bulk UniProt record retrieval</strong><br> To
-      retrieve several uniprot accessions at once, first select <strong>UniProt
-        ID</strong> from the dropdown menu, then paste in the accession IDs as a
-      semi-colon separated list. (e.g. fila_human; mnt_human;
-      mnt_mouse).<br />Hitting Return or OK will automatically fetch
-      those IDs, like the default Sequence Fetcher interface.</li>
+      retrieve sequences for a list of Uniprot accessions, please enter
+      them via the 'Retrieve IDs' tab.</li>
 
     <li><strong><a name="text-search">Complex queries
           with the UniProt query Syntax</a></strong> The text box also allows complex
-- 
1.7.10.2