Step #3

This screen is divided into three areas (from top to bottom) :

the usual control buttons
the trace plot window, showing an x-y plot the pixel values scanned along the selected lane
The trace image window, showing each lane as a straight strip of pixels

The control buttons

On the top row, you find the usual navigator buttons.

Below is a set of buttons to zoom the trace plot. You can specify a zoom percentage explicitly or type it in the yellow box (make sure the mouse pointer in "hovering" over that part of the window).

[100 %] zooms the plot to the same length as the trace image below, which makes it possible to see exactly which region in the plot corresponds to which region on the gel.

NOTE: The zoom functions apply to the plot graph only.

The trace plot sub window

The pixel values scanned along the middle of the lane are displayed as an x-y plot. Furthermore a magnified version of the tracepicture of the selected lane is displayed beneath the plot.

Bands are marked as dots on the peaks of the plot and little triangles facing each other on the lane strip. If there is more than one band on top of a given point, a floating number will warn you about the bands that you can't see. This is only updated when the entire screen is refreshed, not on every addition or deletion of a band, for efficiency reasons. The number may also disappear at higher resolutions if the bands can be seen distinctly.

The current band is marked by a cursor between the triangle markers and a red dot on the plot.

The trace image sub window

Each lane is a pixel strip which has been scanned along the curved lane as seen in Step 2 and straightened out to get this picture of a gel as a block of lanes.

Each lane has a number shown in a black box and a text entry field for its clone name.

This picture cannot be magnified, it is just there to give the user an overview over the current state of the editing - which lane is selected and the position of the currently selected band

At the very left there is a scrollbar to scroll this picture up and down, but the selected lane will always be centered. The bottom sample lane is selected, when you first go to this screen.

Disabling lanes

To disable an entire lane, middle mouse click on the gel image. Note that middle mouse clicking on the clone name will also disable the lane, but will have the additional undesired effect of pasting your buffer contents into the clone name.

Editing the bands

When you enter Step 3, the bottom sample lane and it's first (leftmost) band are selected.

If you want to edit the bands with the mouse, place the mouse pointer somewhere over the plot sub window.
All the editing keystrokes are also active in the trace image sub window.
to edit the clone names, the trace image sub window has to be active.

Navigate the cursor

keys f and b to step one band forward and backwards.
a left mouse click on a band in the plot window selects it.
keys F and B to step through the lanes (backwards and forwards)

Add / Delete bands

a left mouse click on a place on the plot, where there isn't already a band, will create a new one there.
key s to split a band, the old band is shifted slightly to the left and a new band is created to the right.
key d to mark a band as deleted
space key to mark band as good (e.g. if it has been marked as deleted with key 'd' before)
key D to delete a band for good, it is lost now.
a middle mouse click on a band deletes a band for good.
drag the left mouse button to mark an area - answer 'Yes' in the dialog box to remove all band within that area (marked in grey with "doomed bands" in red) from all lanes. It will spare the well band (the first band of each marker lane), so this is an efficient method to delete all bands that are actually background smears before all "real" bands start - position your mouse pointer slightly left of the first real band, press the left mouse button and hold it down, while moving the mouse to the left end of the trace image window until its over the area with the clone name boxes - then release the mouse button and click on "Yes" in the upcoming dialog box.

Shift current band

left and right cursor keys move band by a small distance. Higher zoom modes allow more accurate positioning.
key r will roll the band to its nearest peak - if it was positioned on the side of a band, it'll jump to its top.

Edit clone names

To edit the clone names move your mouse pointer into the trace image sub window.

RETURN key to activate clone name entry field for the current lane./nfs/disk29/fw/data/Chr22c/INCOMING/SC22c1141/
a left mouse click on the clone name entry field activates the lane it belongs to and the entry field itself.
Type the clone name and hit RETURN again and jump to the next sample lane.

NOTE: Every time a clone name field is active, all keystrokes in the trace image sub window will edit the clone name, but all keystrokes sent when the trace plot sub window is active will still edit the bands.

Additional functions

Other functions that may prove useful can be accessed by these keystrokes:

key S to save current band data. Saving the data from time to time might be useful if the machine or the network is unstable and prone to crash, or the program itself decides to present a bug to you and crashes without warning. You can save your work during an editing session with this function.
key R to force Rerunning of the band calling. The upcoming dialog boxes allow you to (a) cancel the request to re-band call and (b) to submit it as a background process in so called "batch" mode. This might be useful if you've gathered new training data and wish to do the band calling again.