Contig-editor

Picking on displayed entities follows the paradigms of the physical map.

In addition there is a control bar at the top of the graph, containing menu- buttons, and a cue. The editor has four menus, which can be selected by picking on the menu buttons.

The control bar has a yellow window displaying the latest-visited position of the scrolling cursor (middle mouse button) in band coordinates.

Cues and information messages are displayed on the right of the control bar.

The map has a scale calibrated in band units.

Setting and Using Marks

A mark is a labelled position on the contig. It is represented by a vertical line through the map, labelled with a band position. The current mark is highlit (yellow).

Most editing operations are carried out relative to a mark. Marks can be set anywhere in the contig, and used to snap to a given part of the contig, which may be off-screen. The simplest way of setting a mark is to line up the scrolling cursor with a feature on the map, and select "Set Mark At Cursor Position".

Marks menu

Utilities menu

Editing Clones menu

Contig-Wide Operations menu

Autopositioning

Operates on two keysets: one specifying the domain of interest for matching, the other the new clones. Generates a report of results which has operations defined on it for surveying and editing positioned clones. After running the autoposition function, the internal cache representing the domain set, and the data of the results of the autoposition function can be saved in separate files for future use. The default domain is the entire database of clones - this does not have to be specified explicitly; and its internal representation can be saved for future use. Generating the internal representation of the domain is a slow operation for large keysets.

The results are displayed on a pad with sensitive areas. This allows picking clones of interest. A pick on a matched clone in the context of the pad causes the clone of interest (the "subject") to be positioned against the match on its contig. The result of this operation can be Edited, Accepted, Rejected, or Bury-ed beneath its match.

Use of accelerators: the following have been defined on the pad, and on the edit panel when autopositioning is in progress.

Fingerprints can be displayed on a separate window, which acts as a scrollable log file.

autopositioning - auto menu on edit panel

autopositioning - report pad menu

Switches

Edit operations

fingerprint window menu

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last edited: July 1994