X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdassettings.html;h=7dc027f7ee0fdb6608056d3e83b7dee3a9f658ba;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=30b36b14f20875e1db82931dd8d82e3b34d1fa00;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html index 30b36b1..7dc027f 100644 --- a/help/html/features/dassettings.html +++ b/help/html/features/dassettings.html @@ -1,32 +1,71 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) +# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle +# +# This file is part of Jalview. +# +# Jalview is free software: you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +# +# Jalview is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty +# of MERCHANTABILITY or FITNESS FOR A PARTICULAR +# PURPOSE. See the GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along with Jalview. If not, see . +#------------------------------------------------------------------------------- - -DAS Settings + + +DAS Settings +

DAS Settings

-

Jalview can retrieve and visualize features from many DAS - sources at once. The DAS sources are discovered and selected via the DAS settings panel.

+

Jalview can retrieve sequences and features from many DAS sources. The DAS sources that +it uses are discovered and selected via the DAS settings panel, +opened either from the View→Feature +Settings dialog box from the alignment window's menu bar, or the Tools→Preferences dialog box +opened from the Desktop menu bar.

The available sources are listed in the table using each source's Nickname as its identifier. Clicking on a source's entry in the table -reveals more information about that service in the panel to the -right. Select the tickbox in the "Use Source" column for a -source to add it to the set Jalview queries for alignment and sequence -features. -

-

You can filter the visible DAS sources by authority, type and "label". - You should read the DAS documentation to understand more about these values. +reveals more information about that service in the panel to the right. +Select the tickbox in the "Use Source" column for a source to +add it to the set Jalview queries for alignment and sequence features.

+

You can filter the visible DAS sources by authority, type and +"label". You should read the DAS documentation to understand +more about these values.

Updating the list of sources

When the DAS Settings panel is first opened, and when the 'Refresh - source' buton is pressed, a list of DAS sources - is retrieved from the DAS registry URL (set by default to the DAS - registration server at - http://das.sanger.ac.uk/registry/das1/sources/).

+source' buton is pressed, a list of DAS sources is retrieved from the +DAS registry URL (set by default to the DAS registration server at +http://das.sanger.ac.uk/registry/das1/sources/).

Adding your own DAS Sources

-

You can add your own DAS source to the list by clicking the "Add Local - Source" button. Enter the URL and nickname of your additional service. - It should be noted that Jalview 2.1 will not query additional sources for more - information, but this will be implemented in future editions. +

You can add your own DAS source to the list by clicking the +"Add Local Source" button. Enter the URL and nickname of your +additional service. It should be noted that Jalview 2.1 will not query +additional sources for more information, but this will be implemented in +future editions.