From: amwaterhouse Date: Fri, 11 Aug 2006 14:19:46 +0000 (+0000) Subject: new files X-Git-Tag: Release_2_1~104 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c0a695cebfd9a86be228472be431096fa9dc281d;p=jalview.git new files --- diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html new file mode 100644 index 0000000..ce11687 --- /dev/null +++ b/help/html/calculations/consensus.html @@ -0,0 +1,13 @@ + +Alignment Consensus Annotation + +

Alignment Consensus Annotation

+

The consensus displayed below the alignment is the percentage of the modal + residue per column. By default this calculation takes includes gaps in column. + You can choose to ignore gaps in the calculation by right clicking on the label + "Consensus" to the left of the consensus bar chart. +

If the modal value is shared by more than 1 residue, a "+" symbol + is used in the display for the simple reason that it is not possible to display + multiple characters in a single character space. + + diff --git a/help/html/features/das.jpg b/help/html/features/das.jpg new file mode 100644 index 0000000..78e061b Binary files /dev/null and b/help/html/features/das.jpg differ diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html new file mode 100644 index 0000000..4e89532 --- /dev/null +++ b/help/html/features/dassettings.html @@ -0,0 +1,26 @@ + + +DAS Settings + + +

DAS Settings

+

Jalview can retrieve features from multiple DAS + sources. The DAS sources are selected in the DAS settings panel.

+

+

On start up of the DAS Settings panel, Jalview will use the registry URL (default + is http://das.sanger.ac.uk/registry/das1/sources/) to retrieve a list of currently + available DAS sources. These are all listed in the table using the sources' + Nickname as an identifier.
+ Click on a Nickname in the table to reveal more information about that service + in the panel to the right of the table. +

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

Tick the box "Use Source" so that Jalview will use a particular source + when fetching features. +

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. +

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