added local das sequence source CLI and documentation

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bb1b7f2..8205374 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -80,13 +80,15 @@ public class Jalview
                       + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                       + "-png FILE\tCreate PNG image FILE from alignment.\n"
                       + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
-                      + "-eps FILE\tCreate EPS file FILE from alignment."
-                      + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
-                      + "-noquestionnaire\tTurn off questionnaire check."
-                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
-                      + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
-                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
-                      + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                      + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+                      + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+                      + "-noquestionnaire\tTurn off questionnaire check.\n"
+                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+                      +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+                      +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+                      + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+                      + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }