X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdassettings.html;h=9600070815f4e9f801960fce5fccd8c77c7c354b;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=b9fe144c2b0f80756dab578882ae8addd363c355;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html index b9fe144..9600070 100644 --- a/help/html/features/dassettings.html +++ b/help/html/features/dassettings.html @@ -1,54 +1,74 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> DAS Settings -

DAS Settings

-

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. -

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/).

-

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. -

  +

+ DAS Settings +

+

+ 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. +

+ 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. Note that the registry hosted at + http://www.dasregistry.org/das/ was retired at the start of 2015. An + alternative service is currently hosted at + http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this + service, ensure your .jalview_properties file includes the following + line:
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/ +

+

+ 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. +