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Examining Results and Using Them to Select Commands

Moving the cursor over plotted results highlights them. The status line gives a brief description of the currently highlighted match. This is in the form:

match name: contig1_number@position_in_contig1, with contig2_number@position_in_contig2, length_of_the_match

For find internal joins the percentage mismatch is also displayed.

Several operations can be performed on each match. Pressing the right mouse button over a match invokes a popup menu. This gives a variety of options, detailed below:

Information
Sends a textual description of this match to the output window.
Hide
Remove this match from the Contig Comparator. The match can be revealed again by using Reveal all within the results manager.
Invoke contig editors
Invoke join editors
Invoke template display
Bring up further displays to show this match in greater detail. For repeat or find internal join matches this will normally be the join editor, or two contig editors when the match is between two points in the same contig. For read pairs two template displays are shown.
Remove
Removes this match from the Contig Comparator. The match cannot be revealed again by using Reveal all within the results manager.

One of the items in the popup menu may have an asterisk next to it. This is the default operation which can also be performed by double clicking the left mouse button on the match.

The crosshairs can be toggled on and off and a diagonal line going from top left to bottom right of the plot can also be displayed if required. This is useful as a guide for moving the contigs such that their matches lie upon the diagonal line.

The "Results" menu on the contig selector window provides a similar mechanism of accessing results, but at the level of all matches in a particular search. This is simply a menu driven interface to the results manager window (see section Results Manager), but containing only the results relevant to the contig comparator window.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_41.html