Editing In Selection Areas

From: jprocter Date: Mon, 10 Apr 2006 11:31:10 +0000 (+0000) Subject: doco X-Git-Tag: Release_2_08~26 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=360dd77948165056e37da01dc25e07a467c838ae;p=jalview.git doco --- diff --git a/help/help.jhm b/help/help.jhm index f3d96c4..fcfc0a8 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -25,7 +25,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index cc3555e..62cba6b 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -5,7 +5,7 @@ + target="edit.selareas"/> diff --git a/help/html/editing/index.html b/help/html/editing/index.html index bcb4e94..a33dea7 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -14,12 +14,14 @@ href="../keys.html">keystrokes table.

Tip: For large alignments, deselect "Calculate -> Autocalculate Consensus" to prevent the alignment performing lengthy calculations after every edit.

Inserting / removing gaps - hold down the "Shift" key. Click - a residue with the mouse and drag the residue to the right to insert gaps or - to the left to remove gaps.
- If the residue selected is within a defined group, hold down either "Control" +

Inserting / removing gaps - hold down the + "Shift" key. Click on a residue with the mouse and drag it + to the left or right to insert gaps and remove gaps.
+ If the current selection is a group over all sequences in the + alignment, or a group over some sequences or all columns in the + alignment, then hold down either "Control" key and drag the residue left or right to edit all sequences in the defined - group at once.

+ group at once.

Copy/paste/cut/delete - any sequences which are in the current selection box (indicated in red) may be cut and / or copied to a new alignment or deleted.

diff --git a/help/html/editing/selectionAreas.html b/help/html/editing/selectionAreas.html new file mode 100755 index 0000000..384d6fa --- /dev/null +++ b/help/html/editing/selectionAreas.html @@ -0,0 +1,18 @@ + + +Editing In Selection Areas + + +

Editing In Selection Areas

+ Editing can be restricted to the current + selection area. This allows the user to "Lock" the alignment either + side of the selection area. Any gap insertions or deletions will only affect + the current selection area.

In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, + the same number of gaps will be inserted at position 116, (between M and L). +

+ +

Locked selection area based editing was introduced in Jalview 2.08

+ + diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html new file mode 100755 index 0000000..31369d8 --- /dev/null +++ b/help/html/features/featuresettings.html @@ -0,0 +1,43 @@ + + +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.

Sequence Feature + Settings for the Jalview Application +

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 + colour and whether they are currently being displayed (only the + ticked features and groups are displayed). You can change the + colour used for a feature in the associated alignment by clicking on + its colour box.

Transparency and Feature Ordering

+ 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).

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.

+ The transparency slider setting (currently only available + in the application version) 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.

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

+ +