5.5 Band Fragment-Size Editing

Fragment sizes may be edited on an intralane or across-lane basis. Both marker and experiemntal band sizes may be edited. This size-edit feature is designed for making small, incremental changes to sizes; you may find it cumbersome for making large changes. For large changes, editing of the placement of the band is recommended. Selecting the Size Edit button pops a menu from which one chooses horizontal (across lanes) or vertical (intralane) editing. From the Commands Menu, click [Operations] ; then click [Size Edit . The Size Edit Popup appears, as in Figure 5.5. The [Edit Vertical] and [Edit Horizontal] buttons are explained below. Clicking the [Cancel] button removes the Size Edit Popup.

Figure 5.5: The Size Edit Popup.

5.5.1 Edit Vertical

If you click [Edit Vertical] , the Size Edit Popup menu disappears. A Vertical Size Edit Popup (Figure 5.6) appears to the right of the image. Clicking its [Done] button at any time removes this popup and returns control to the Operations Submenu. Everything below the \fbox{Done} button refers to a single lane within the image; by default, the leftmost lane of the image is represented when the popup first appears.

Figure 5.6: The Vertical Size Edit Popup.

Below the [Done] button are 3 colored stripes containing the labels from the lane-label, inheritance, and lane index stripes for the lane involved. In Figure 5.6: the lane-label is "M" (for marker lane); the inheritance-label is blank denoting that this lane is not a family member; and the lane-index label is "0" (index position "0").
Lanes are changed with 5 buttons below the labels.

For any lane, below these 5 buttons, are displayed horizontal bars to indicate the relative locations of bands in that lane. If the lane is a marker lane, these bars are colored red; otherwise, the bars are colored green. Next to each bar is the fragment size displayed in a box. Where the bands are tightly packed, the boxes containing the fragment sizes may be spread out, as is the case in Figure 5.6.
To edit any size, click in the box containing the size. A pair of buttons, [+] [-] , appears next to the box containing the size to be edited. In Figure 5.6, this pair is next to the box showing fragment size = 11. Sizes are incremented or decremented by clicking these [+] and [-] buttons. The upper limit of increment is 1 less than the size of the next band; if there are no higher-sized bands, there is no upper limit. The lower limit is 1 more than the size of the next lower band; if there are no lower-sized bands, the lower limit is 0. Size changes are effective immediately and cannot be automatically reset. Editing ceases when [Done] is clicked.

5.5.2 Edit Horizontal

If you click [Edit Horizontal] , the Size-Edit popup menu disappears. Two thin blue horizontal lines span the image, extending from the left of the image to the top and bottom of the scroll thumb in the vertical scrollbar to the right of the image. By moving the scroll thumb up or down with MB2, the thin blue lines move along. An example appears in Figure 5.7. These lines bracket a region of interest whose fragment sizes appear the Horizontal Size Edit Popup as in Figure 5.8. The blue lines are separated by a vertical distance of 7 pixels.

Figure 5.7: Horizontal Size Edit Bracket Lines in the Primary Image.

The Horizontal Size Edit Popup appears above the image. This popup consists of a rectangular grid of tiles. The grid width corresponds to the number of lanes on the image. The grid height is 10 tiles; the top 3 tiles are for representing the same labels as those of the lane-index, lane-label, and inheritance stripes for a given lane while the bottom 7 are for fragment sizes of bands appearing between the two blue horizontal lines in that lane. The 7 tiles correspond to the 7 pixels separating the blue lines.

Figure 5.8: The Horizontal Size Edit Popup.

Move the scroll thumb up or down until it includes several bands in several lanes. Note the sizes in the tiles within the popup above the image. To change the value of any fragment size, click in the tile containing that size. Appearing above the tile will be two small buttons: [+] [-] . Click in either of these and the size will increment or decrement by one. You may continue clicking (incrementing or decrementing) until the size is correct. The upper limit of increment is 1 less than the size of the next band within the lane; if there are no higher-sized bands, there is no upper limit. The lower limit is 1 more than the size of the next lower band; if there are no lower-sized bands, the lower limit is 0. Size changes are effective immediately and cannot be automatically reset.
> Above the grid are three buttons: [Done] -- [+] -- [-] . Clicking [+] moves the scroll thumb and two blue lines 1 pixel down in the image while clicking [-] moves them 1 pixel up. Clicking [Done] removes the Horizontal Size Edit poup and returns control to the Operations Submenu.


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