JAL-629 more docs

[jalview.git] / help / help / html / features / clarguments-ng.html

diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html
index 4a173d2..5f2ef5a 100644 (file)
--- a/help/help/html/features/clarguments-ng.html
+++ b/help/help/html/features/clarguments-ng.html
@@ -25,6 +25,11 @@
   <h1>Jalview Command Line Arguments (version 2.11.3.0 and later)</h1>
 
   <p>
+  For a summary of Jalview command line arguments see <a href="clarguments-ng-summary.html">Summary
+  of Command Line Arguments</a>.
+  </p>
+  
+  <p>
   From version 2.11.3.0 Jalview processes a new set of command line arguments
   which allow more powerful and flexible combinations of arguments, though can
   also be used for very simple use cases too.
@@ -73,7 +78,7 @@
   in typical use cases you may still want to think of it as doing so.
   <br/>
   For more advanced use please see
-  <a href="advancedclarguments.html">Advanced Command Line Arguments</a>.
+  <!--<a href="advancedclarguments.html">Advanced Command Line Arguments</a>.-->
   </p>
 
 
@@ -82,7 +87,7 @@
   <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h4>
 
   <p>
-  To simply open one or more alignment files in different frames just put the filenames as the first arguments:
+  To simply open one or more alignment files in different windows just put the filenames as the first arguments:
   <pre>
   jalview filename1 filename2 ...
   </pre>
@@ -104,10 +109,10 @@
   after the initial filenames.)
   </p>
 
-  <h5 name="--open"><code>--open</code></h5>
+  <h5 name="open"><code>--open</code></h5>
 
   <p>
-  Use the <code>--open</code> argument to open alignment files each in their own frame.
+  Use the <code>--open</code> argument to open alignment files each in their own window.
   </p>
 
   <p>
@@ -130,14 +135,14 @@
   </pre>
   </p>
 
-  <h5 name="--append"><code>--append</code></h5>
+  <h5 name="append"><code>--append</code></h5>
 
   <p>
   To append several alignment files together use:
   <pre>
   jalview --open filename1.fa --append filename2.fa filename3.fa
   </pre>
-  or, if you haven't previously used <code>--open</code> then you can use --append to open one new frame and keep appending each set of alignments:
+  or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
   <pre>
   jalview --append these/filename*.fa --append more/filename*.fa
 
@@ -146,13 +151,13 @@
   </p>
 
   <p>
-  <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original frames and not append to another.
+  <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
   </p>
 
-  <h5 name="--new"><code>--new</code></h5>
+  <h5 name="new"><code>--new</code></h5>
 
   <p>
-  To append different sets of alignment files in different frames, use <code>--new</code> to move on to a new alignment frame:
+  To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
   <pre>
   jalview --append these/filename*.fa --new --append other/filename*.fa
   </pre>
@@ -232,7 +237,7 @@
   <h5 name="annotations"><code>--annotations</code></h5>
 
   <p>
-  You can specify whether the currently opened alignment frame should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>.  If you don't specify then your saved preference will be used.
+  You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>.  If you don't specify then your saved preference will be used.
   <pre>
   jalview --open examples/uniref50.fa --noannotations
   </pre>
@@ -241,7 +246,7 @@
   <h5 name="title"><code>--title</code></h5>
 
   <p>
-  If you would like to give the alignment frame a specific title you can do so with the <code>--title</code> option:
+  If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
   <pre>
   jalview --open examples/uniref50.fa --title "My example alignment"
   </pre>
@@ -250,7 +255,7 @@
   <h5 name=""><code>--structure</code></h5>
 
   <p>
-  You can add a 3D structure file to a sequence in the current alignment frame with the <code>--structure</code> option:
+  You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
   <pre>
   jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
   </pre>