| Menu |
Function |
Button/Key |
Action |
Constraints |
| File |
New Project |
ctrl-N |
Open a file and display
the alignment in the window in a new tab |
Only .col and .widetext
format is supported. |
| File |
Open Project |
ctrl-O |
Opens an existing project
and displays it on the screen in a new tab |
|
| File |
Close a project |
ctrl-W |
Closes the active alignment
tab |
|
| File |
Save project |
ctrl-S |
saves the current state
of the alignment including colors and fonts |
|
| File |
Delete project |
'Delete' button |
Deletes all files associated
with the given project, but does not delete original files, because
the project files are imported into a separate directory structure. |
|
| File |
Save alignment as.. |
|
Export an alignment.
Saves the alignment to a location of your choice, with a filename
of your choice |
widetext, col and fasta
formats supported |
| Edit |
Undo |
ctrl-Z |
Undo the last undo-able
action
|
Se below for which functions
supports undo |
| Edit |
Redo |
ctrl-shift-Z |
Redo the last undone
action
|
Se below for which functions
supports redo |
| Edit |
Move left |
 |
|
|
| Edit |
Move right |
 |
|
|
| Edit |
Change symbol |
 |
Changes the selected symbol(s) to the entered symbol |
Sequences can only contain: A,a,U,u,T,C,c,G,g,-,B,D,K,M,N,R,S,V,W,X,Y |
| Edit |
Pair bases |
 or ctrl-B |
If pairing bases Changes
lowercases to uppercases and resolves the pairingmask. If unpairing
bases changes to lowercase. |
|
| Edit |
Pair columns |
 |
|
|
| Edit |
Go to .. |
Ctrl-J |
Type in the columnnumber.
The view changes to show the entered column |
when in split
view the column is shown in the right/bottom vindow. |
| Edit |
History |
|
When selecting a history
window opens for each open project. Use of history window: click
on a file-name to change the alignment back to that file. click
on a command to go back to that command. Changes the alignment back
to the given point.
|
Not all commands can
be undone and redone, see below for a complete list. |
| View |
Colors |
|
Select the character-type
or selection type you want to change color for. Changes the applications
alignment coloring. |
Limited to the color
shown |
| View |
Single select |
 |
changes the selection
mode of the application. In 'Primary selection' mode the selected
base is the only one selected. In 'Both' selection mode the complementary
base is also selected, and shown in the window. |
This affects only splitview.
Primary selection mode only allows selection in the left/upper window. |
| View |
Double select |
 |
changes the selection
mode of the application. In 'Primary selection' mode the selected
base is the only one selected. In 'Both' selection mode the complementary
base is also selected, and shown in the window. |
This affects only splitview.
Primary selection mode only allows selection in the left/upper window. |
| View |
Operation mode |
|
changes the operation
mode of the application.
In 'primary selection' operation mode only the primary selection
is changed by the actions. In 'secondary selection' operation mode
only the secondary selection is changed by the actions. In 'both
' operation mode both the primary and the secondary selection is
changed by the actions. |
Works only in splitview
mode |
| View |
Split mode |
|
Descide
if the vindow split vertically or horizontally when split. |
|
| View |
Split
screen
|
 or ctrl-2 |
Splits
the screen horizontally or vertically |
|
| View |
Unsplit
screen
|
 or ctrl-1 |
Unsplits
the screen
Constraints: |
|
| View |
Fonttype
|
|
Changes
the fonttype for the alignment. |
Only
the included fonts can be selected |
| View |
Fontsize |
|
Changes
the fontsize for the alignment. |
Only
fontsizes between 8 and 16 can be chosen. |
| View |
Clear
Selections |
ctrl-shift-C
|
Clears
all selections |
|
| View |
Tablegrid
|
|
When
selected a grid is shown seperating the individual bases |
|
| View |
Fixed
scrolling |
|
When
selected the two tables in splitview follow each other when scrolled
vertically. In vertically splitmode the two alignment show the same
sequences across the screen. |
|
| View |
Base
coloring |
|
When
selected the different bases are drawn in different colors
When deselected all bases have the same color. |
T,t,u
and U are in the same color. |
| View |
Overview |
|
When
selected an overview-window for each open project is showing.
You can zoom in using the '+' button and zoom out using the '-'
botton. The fit button trys to fit the alignment into the window
but wil not go bolow zoom-level 1, where one base is one pixel. |
|
| Tools |
Programs |
f9 |
Runs
the program(s) selected from the pop-up window |
|
| Tools |
Adding
sequences |
|
Add
the sequences contained in the file selected from the pop-up window |
Sequences
with an already existing name is not imported |
| Tools |
Deleting
sequences |
|
Removes
the sequences from the alignments |
|
| Tools |
Adding
Columns |
|
Inserts
a column at a given position, the column consists solely of gaps'-' |
Only
one column can be added at at one time |
| Tools |
Remove column |
|
Removes
a given column from the alignment |
Only
one column can be removed at one time |
| Tools |
Remove
coloring |
|
Removes
any analysis-coloring from alignment |
|
| Tools |
Removing
gaps |
|
Removes
any column that consists solely of gaps |
|
| Tools |
Empty
pairingmask |
|
|
|
| Tools |
Fit alignment to pairingmask |
|
Changing
upper/lower cases to corresponds to pairngmask. Fits the alignment
to the pairingmask by changing all letters inside pairingmask to
uppercase and all others to lowercase |
|
