Cursor Mode

From 4e377b5c02352a12537100dddd2f8a2b84536205 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 6 Apr 2006 17:02:12 +0000 Subject: [PATCH] added cursorMode feature page and rearranged keystrokes documentation. --- help/help.jhm | 1 + help/html/features/cursorMode.html | 53 ++++++++++++++++++ help/html/keys.html | 104 ++++++++++++++++++++---------------- help/html/whatsNew.html | 2 +- 4 files changed, 113 insertions(+), 47 deletions(-) create mode 100755 help/html/features/cursorMode.html diff --git a/help/help.jhm b/help/help.jhm index 21e28ad..2a479e9 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -7,6 +7,7 @@ + diff --git a/help/html/features/cursorMode.html b/help/html/features/cursorMode.html new file mode 100755 index 0000000..5172cfa --- /dev/null +++ b/help/html/features/cursorMode.html @@ -0,0 +1,53 @@ + + +Cursor Mode + + +

Cursor Mode

Cursor mode is a new feature in Jalview 2.08, and allows more +precise selection and editing of alignments through the use of the +keyboard for both navigation and the input of editing and selection commands.

F2 Toggles between normal and cursor editing modes. When +in cursor mode, a black cursor appears in the residue area of the +alignment, and any mouse clicks on that area will move the cursor to +that position (this means that the region selection menu is +unavailable in cursor mode).

Navigation +

Cursor keys - Move cursor around the alignment.

S - Type a number x then press 'S' to jump to sequence x.

C - Type a number x then press 'C' to jump to column x.

P - Type a number x then press 'P' to jump to position x in current sequence.

65,82<return> - Quick jump to column 65, sequence 82

Defining Regions +

Q - Define the top left corner of the selection area

M - Define the bottom right corner of the selection area
+

Editing The Alignment +

Space - Insert a gap at the cursor position.
+ To insert 12 spaces at the current cursor, type 12 before pressing Space.
+ To group insert, hold control or shift together with space.

Delete - Delete a gap at the cursor position.
+ To delete 12 spaces at the current cursor, type 12 before pressing Delete.
+ To group delete, hold down control or shift together with Delete.

+ + diff --git a/help/html/keys.html b/help/html/keys.html index 1b0339c..33651d6 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -2,52 +2,64 @@ Key Strokes

Key Strokes

Jalview recognises the following keystrokes.

Escape - Clears the current selection region, highlighted columns and highlghted - residues

Control 'A' - Selects all sequences in the alignment.

Control 'C' - Copies the selected region, in Fasta format (Not applet, as no - clipboard is available)

Control 'V' - Pastes the selected file (Can be external to Jalview) to a new - alignment window.

Control 'X' - Cuts the selected region from the alignment window.

Control 'Z' - Undoes the last sequence edit.

Control 'F' - Launches the search window.

Up Arrow - Moves selected sequence(s) up the alignment

Down Arrow - Moves selected sequence(s) down the alignment.

F1 - Show Help Documentation

F2 - Toggle Cursor mode on / off

With Cursor mode on....

Cursor keys - Move cursor around the alignment.

Space - Insert a gap at the cursor position.
- To insert 12 spaces at the current cursor, type 12 before pressing Space.
- To group insert, hold control or shift together with space.

Delete - Delete a gap at the cursor position.
- To delete 12 spaces at the current cursor, type 12 before pressing Delete.
- To group delete, hold down control or shift together with Delete.

S - Type a number x then press 'S' to jump to sequence x.

C - Type a number x then press 'C' to jump to column x.

P - Type a number x then press 'P' to jump to position x in current sequence.

Q - Define the top left corner of the selection area

M - Define the bottom right corner of the selection area
-
65,82<return> - Quick jump to column 65, sequence 82

+Jalview responds a number of key strokes, and has two distinct modes of +keyboard operation. The F2 key switches between 'Normal' and +'Cursor' mode operation. +

+ + + + + + + + +As in normal mode, but also cancels any partially entered commands + + +Show Help Documentation + + + + + + + +Moves selected sequence(s) up the +alignment + +Moves selected sequence(s) down the +alignment. + + + + + + +Pastes the contents of the clipboard +to a new + alignment window. (same as the Alignment Window menu Edit->Paste + command)
nb. if the paste is from a Jalview alignment, any + sequence and alignment annotations will also be copied over. + + + + + + +

Key	Which Mode	Action
+Escape	Normal	Clears the current selection region, +highlighted columns and highlghted residues. +
Escape	Cursor
F1	Both
F2		Toggle Cursor mode on / off
Control 'Z'	Both	Undoes the last sequence edit
Up Arrow	Normal
Down Arrow	Normal
Control 'A'	Both	Selects all sequences in the alignment
Control 'C'	Both	Copies the selected region into +the clipboard as a Fasta format file nb. not available in applet, as no clipboard is available
Control 'V'	Both
Control 'X'	Both	Cuts the (fully) selected +sequences from the alignment.
Control 'F'	Both	Launches the search +window

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 8c28564..7fa9806 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -5,7 +5,7 @@

Jalview Version 2.08

Editing can be locked to the selection area. Any edits made within the locked area do not affect the rest of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list +

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list of keyboard controls, look here.

Create sequence features from searches. Previously results from searches were added as alignment positions, which was -- 1.7.10.2