X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=fa273a5d1cf58f2dc6632ca1707de0890bfbe52c;hb=b11a3470c5ccd9eeb4e80c1e85b282dcc8111b4a;hp=63a14af6c91f54089dc638f32c30b034a3f596bd;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 63a14af..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.
|
@@ -96,41 +96,28 @@
- -nousagestats
- |
- Turn off google analytics usage tracking
- |
-
-
+ -nonews
- -[no]sortbytree
- |
- Enable or disable automatic sorting of
- associated view when a new tree is displayed
+
+ Disable check for Jalview
+ news on startup (not recommended other than for classroom /
+ demo usage)
+
|
- -dasserver nickname=URL
+ -nousagestats
|
-
- 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
-
+ Turn off google analytics usage tracking
|
- -fetchfrom nickname
+ -[no]sortbytree
|
-
- Query a DAS source called
- nickname for features for the alignments and display them
-
+ Enable or disable automatic sorting of
+ associated view when a new tree is displayed
|
@@ -247,6 +234,14 @@
Create Scalable Vector Graphics
file FILE from alignment. |
+
+ -biojsMSA FILE |
+
+ |
+