X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;fp=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=0000000000000000000000000000000000000000;hb=aace9d05c0870c703bfdfb28c1608213cee019bf;hp=3d7c944b864b78c32f40afa078e26db841489b10;hpb=2a3bac30ae8290e912eb7ffe7ff7ec700b6cfaac;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html deleted file mode 100755 index 3d7c944..0000000 --- a/help/html/features/featuresettings.html +++ /dev/null @@ -1,132 +0,0 @@ - - - -Sequence Feature Settings Dialog Box - - -

- Sequence Feature Settings Dialog Box -

-

- Select View→Feature Settings... menu entry in - an alignment window to open the feature settings dialog box, which - allows you to precisely control the presence and appearance of - sequence features for the current alignment. -

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- Sequence Feature Settings for the Jalview Application -
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- The top section of the dialog box lists all the sequence feature - groups, along with a tickbox for each that controls whether its - features are displayed. The table in the middle lists all the - features in the currently selected groups, along with their display - style and whether they are currently being displayed (only the - ticked features and groups are displayed). You - can change the colour or shading style used for a feature in the - associated alignment by clicking on its colour box. -

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- Selecting - alignment columns by feature
Double-clicking - a feature type in the Feature Settings dialog - allows you to select columns in the alignment that contain (or do - not contain) features of that type. If a region of the alignment is - currently selected, then only features in the current selection will - be searched. The following keys affect the way in which selections - are made: -

- Options are also provided in the feature's pop-up menu (see below). -
- Select columns by feature was added in Jalview 2.8.1 -

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- Feature settings pop-up menu
Right-click - on a feature to open a pop-up menu that allows you to -

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- Features may be highlighted with either a single colour or a feature colourscheme based on - either the scores associated with that feature or from the feature's - description (e.g. to distinguish different names associated with a - DOMAIN feature). -

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- Ordering alignment by - features
The 'Seq Sort by Score' and 'Seq Sort by - Density' buttons will sort the alignment based on the average score - or total number of currently active features and groups on each - sequence. To order the alignment using a specific feature type, use - the sort by .. entries in the pop-up menu for that type.
- Feature sorting and graduated feature colouring were - introduced in Jalview 2.5 -

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- Transparency and Feature Ordering -

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It is important to realise that sequence features are often not - distinct and often overlap (for example, a metal binding site - feature may be attached to one position along a stretch of sequence - marked with a secondary structure feature).

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- The ordering of the sequence features in the dialog box list is the - order used by Jalview for rendering sequence features. A feature at - the bottom of the list is rendered below a feature higher - up in the list.
You can change - the order of a feature by dragging it up and down the list with - the mouse (not applet). -

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- The Optimise order button (currently only - available in the application) will re-order the feature render - ordering based on the average length of each feature type. -

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- The transparency slider setting controls - the visibility of features rendered below other features. Reducing - the transparency will mean that features at the top of the list can - obscure features lower down, and increasing it allows the user to - 'see through' the upper layers of a set of features. -

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- You can save all features, with their - current colours and visibility in a Jalview format file. -

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