Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=e8fce8419dd2d08a6769acb936cc36a2b2e1fcaf;hb=27ff898c1881430653df81a8f0ff218cd2052f7a;hp=608854617552d7b9a394015c9dbcf23c02380758;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 6088546..e8fce84 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,75 +1,67 @@ - -Alignment Window Menus - - -

Alignment Window View Menu

View

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Font
- Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
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Wrap
- When ticked, the alignment display is "wrapped" - to the width of the alignment window. This is useful if your alignment has - only a few sequences to view its full width at once.
- Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each - sequence row.
- NOTE: When in wrapped alignment view, the alignment cannot - be edited or have regions selected on it.
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Show Full Sequence ID
- If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format NAME/START-END
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Boxes
- If this is selected the background of a residue will be coloured using the - selected background colour. Useful if used in conjunction with "Colour - Text."
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Text
- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
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Colour Text
- If this is selected the residues will be coloured according - to the background colour associated with that residue. The colour is slightly - darker than background so the amino acid symbol remains visible.
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Show Gaps
- When this is selected, gap characters will be displayed as - "." or "-". If unselected, then gap characters will - appear as blank spaces.
- You may set the default gap character in preferences.
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Show Annotations
- If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the conservation - calculation, quality calculation and consensus values as bar charts.
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Sequence Features
- If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features - from the EBI. Features which are 1 residue in length are coloured red, sequences - longer than 1 residue are coloured blue. Move the mouse over a coloured - feature to display the details of the feature.
- Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
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Seqence Settings
- If features have been added to the alignment then the priority of rendering - the features can be altered so that overlapping features can be displayed - or hidden. See Sequence Features.
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Overview Window
- A scaled version of the alignment will be displayed in a small - window. A red box will indicate the currently visible area of the alignment. - Move the visible region using the mouse.
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- - + + + +Alignment Window Menus + + + +

Alignment Window View Menu

New View (Control T)
+ Creates a new view from the current alignment view.
Expand Views (X)
+ Display each view associated with the alignment in its own alignment window, + allowing several views to be displayed simultaneously.
Gather Views (G)
+ Each view associated with the alignment will be displayed within its own tab + on the current alignment window.
Show→(all Columns / Sequences / Sequences and Columns )
+ All hidden Columns / Sequences / Sequences and Columns will be revealed.
Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
+ Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
Automatic Scrolling
+ When selected, the view will automatically scroll to display the + highlighted sequence position corresponding to the position under the mouse + pointer in a linked alignment or structure view. +
Show Sequence Features
+ Show or hide sequence features on this alignment.
Sequence Feature Settings...
+ Opens the Sequence Feature Settings dialog box to control the colour and display + of sequence features on the alignment, and configure and retrieve features + from DAS annotation servers.
Sequence ID Tooltip (application only) +
This submenu's options allow the inclusion or exclusion of + non-positional sequence features or database cross references + from the tooltip shown when the mouse hovers over the sequence ID panel.
Alignment Properties...
+ Displays some simple statistics computed for the + current alignment view and any named properties defined on the + whole alignment.
Overview Window
+ A scaled version of the alignment will be displayed in a small + window. A red box will indicate the currently visible area of the alignment. + Move the visible region using the mouse.

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