X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=da045bacce7da83c8356d8c76596c659f3d6a4e5;hb=550949340ef5ccd5757dd50b11b9613d61571046;hp=4af43dea3bce266b7bb45ed85c816b039548c18e;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 4af43de..da045ba 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -46,8 +46,13 @@ and displaying structure information.
  • The "Connections" - Preferences tab allows you to change the links made from Jalview - to your default web browser. + Preferences tab allows you to configure Jalview's internet + settings and specify your default web browser. +
    • +
  • The "Links" + Preferences tab shows the currently configured URL + Links shown in the Link submenu in the Sequence + ID popup menu.
  • The "Output" Preferences tab contains settings affecting the export of @@ -63,8 +68,8 @@
  • The "Web Service" Preferences tab allows you to configure the JABAWS servers that Jalview uses, and change the layout of the + href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS + servers that Jalview uses, and change the layout of the alignment's Web Services menu.
    • @@ -78,9 +83,8 @@

    Open Overview Window - When this is selected, the alignment overview panel is opened by default for a new alignment - window. + href="overview.html">alignment overview panel is opened + by default for a new alignment window.

    Show Annotations - If this is selected the new window will @@ -155,9 +159,9 @@ Open file - If this is selected then the default alignment file will be opened when Jalview is started. You can change the default file by clicking on file name and either typing in the file - path or selecting it from the file chooser window.
    - Note: The default example alignment is updated periodically - to demonstrate new features in Jalview. + path or selecting it from the file chooser window.
    Note: + The default example alignment is updated periodically to + demonstrate new features in Jalview.

    "Colours" @@ -172,9 +176,9 @@

    Annotation Shading Default - set the default minimum and maximum colours used when Colour by Annotation... is selected from the alignment window's - colours menu. + href="../colourSchemes/annotationColouring.html">Colour + by Annotation... is selected from the alignment window's colours + menu.

    "Structure" @@ -213,13 +217,6 @@ Preferences tab

    - URL Link From Sequence ID
    These definitions are - used to generate URLs from a sequence's ID or database cross - references. Read more about configuring URL links here. -

    -

    Default Browser (Unix)
    Its difficult in Java to detect the default web browser for Unix users. If Jalview can't find your default web browser, enter the name or full path to your web @@ -241,6 +238,33 @@ statement for more information.

    + The "Links" Preferences + tab +

    +

    + This panel shows a table, and two sections - Edit and Filter. + The table shows the available URL link definitions (consisting of a + database, Name, and URL template string), a checkbox In + Menu which indicates if the link is enabled, and Double + Click which marks the link that will be opened if a sequence's ID + is double clicked. The table can be sorted by clicking on the column headers. +

    +

    Edit Links
    This section contains three buttons, + New, Edit and Delete, which allow you to + create, modify and remove user-defined URL links from the Sequence + ID's links submenu. +

    +

    + Filter
    The Filter text box allows you to + quickly show rows in the table containing a particular text string. + The Custom only button limits the entries in the table to + just those you have configured yourself via the Edit + Links buttons. Press Show all to clear any filters. +

    + Read more about configuring + URL links. +

    +

    Output Preferences tab

    @@ -292,11 +316,10 @@

    When this option is enabled, Jalview embeds BioJSON data within HTML files exported from Jalview at - generation time. This enables the exported HTML files to be - extracted and imported back into the Jalview desktop application at - a later time. + href="bioJsonFormat.html">BioJSON data within HTML files + exported from Jalview at generation time. This enables the exported + HTML files to be extracted and imported back into the Jalview + desktop application at a later time.

    Use Modeller Output

    @@ -309,7 +332,7 @@ and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected.

    - Editing Preferences tab + e"Editinge" Preferences tab

    There are currently three options available which can be selected / deselected.