X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=fa273a5d1cf58f2dc6632ca1707de0890bfbe52c;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=1d6f62d2588fca8f41a58ac4d029d1ae12f86fc4;hpb=27c7530b396a5dd1addc4ab346ef2823d34fb335;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 1d6f62d..fa273a5 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -67,8 +67,8 @@
-annotations FILE/URL
Add precalculated annotations to the alignment. See Annotation File description.
+ href="annotationsFormat.html" target="NEW">Annotation
+ File description.
|
@@ -98,7 +98,11 @@
-nonews
|
- Disable check for Jalview news on startup (not recommended other than for classroom / demo usage)
+
+ Disable check for Jalview
+ news on startup (not recommended other than for classroom /
+ demo usage)
+
|
@@ -118,30 +122,6 @@
- -dasserver nickname=URL
- |
-
- Add and enable a DAS server
- with given nickname (alphanumeric or underscores only) for
- retrieval of features for all alignments Sources that
- also support the sequence command may be specified by
- prepending the URL with 'sequence:' e.g.
- sequence:http://localdas.somewhere.org/das/source
-
- |
-
-
-
- -fetchfrom nickname
- |
-
- Query a DAS source called
- nickname for features for the alignments and display them
-
- |
-
-
-
-groovy FILE/URL
|
Execute groovy script in FILE (where
@@ -254,6 +234,14 @@
Create Scalable Vector Graphics
file FILE from alignment. |
|
+
+ -biojsMSA FILE |
+
+ |
+