## 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

- Set Mark At Cursor Position: set a mark at the current cursor position
- Mark Centre: set a mark at the current centre of graph
- Mark Centre Of Cosmid: set a mark at the centre of the current cosmid
- Set Mark: set a mark at a specified band coordinate
- Zero Scale To Mark: recalibrate the scale with current mark=0 - this does not change the model
- Set Scale At Mark: recalibrate the scale with current mark= specified band coordinate - this does not change the model
- Reset Scale: restore original calibration of the scale
- Snap To Mark: display graph centred on current mark
- Snap To Previous Mark: display graph centred on previous mark: this allows toggling repeatedly between the latest two marks set
- Visit Mark: display graph centred on each mark set, in turn, in reverse order
- Delete Mark: delete current mark (this will occur even if it is off-screen)
- Delete All Marks: you guessed it

### Utilities menu

- Overview Physical Map: peek at the default physical map display, preserving the state of the editor - useful for fast scrolling using the physical map's mini-contig
- Finished Edit: finish editing session, and revert to the default physical map
- Quit: quit this physical map - like Quit on the default map
- Help: what you are reading
- Print: PostScript dump of the edit panel
- Preserve: as elsewhere
- Redraw: as elsewhere
- Remarks: vary the density of remarks displayed in the edit panel: this is a switch with three states
- Recalculate: as elsewhere
- Unhighlight, Revert: clean the edit panel - remove all highlighting, editing marks, etc and restore the default level of remarks

### Editing Clones menu

- Left End Of Clone To Mark: move the currently-selected clone so that its left end abuts the current mark
- Right End Of Clone To Mark: move the currently-selected clone so that its right end abuts the current mark
- Extend Left End Of Clone To Mark: extend the currently-selected clone so that its left end abuts the current mark
- Extend Right End Of Clone To Mark: extend the currently-selected clone so that its right end abuts the current mark
- Show Buried Clones Of Clone: show buried clones of currently-selected clone - they are not automatically positioned at present
- Show All Buried Clones: show all buried clones of the contig - they are not automatically positioned at present
- Attach Clone: introduce a YAC or cosmid into the contig
- Detach Clone: detach the currently-selected YAC or cosmid from the contig

### Contig-Wide Operations menu

- Open Contig: The contig is cut at the current mark, and one side positioned relative to the other by dragging it left or right with the left mouse button down, to compress or extend the contig at the mark. A crosshair marks the current cursor position. The current position of the moving side of the cut is displayed in the cue, and the current position of the cross-hair cursor is displayed in the yellow position box in the control bar. When the contig is recalculated, a new mark is placed automatically at the final position of the moving side of the cut, and the position of all affected marks is updated. F4 has the function of an UNDO key for this operation: you can interrupt and back off this operation.

### 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.

- UP, DOWN arrow keys: previous, next match for the current subject
- LEFT, RIGHT arrow keys: skip to results for previous, next subject
- 'a': accept this match (adds subject to the contig)
- 'r': reject this match
- 'e': add the subject to the contig as displayed, for manual edit
- 'b': bury the clone under its match

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

### autopositioning - auto menu on edit panel

- Autoposition Clones from Keyset: use current keyset
- Set Autoposition Domain: use current keyset to define domain of Autoposition operation
- Load Domain: load internal representation of domain from named file
- Use Whole Database: implicit argument
- Save Domain: in a named file
- Load Results: load data of previous Autoposition from named file A results file cannot be loaded without loading an appropriate domain file.
- Save Results: in a named file
- Fingerprint: show fingerprint of the currently-selected clone

### autopositioning - report pad menu

- Quit:
- Help:
- Print:
- Preserve:
- Save Results:
- Save Domain:
- Tree:

Switches

- Set to Edit: the default behaviour of the accelerator keys is to advance to the next match (or next subject's first match) and position against that: when this switch is set, the latest match is displayed on the edit panel after using the accelerators, instead
- Show Fingerprints: when this switch is set, clone fingerprints are displayed automatically in the Fingerprint window whenever a clone on the report is selected, or the accelerators are used

Edit operations

- Accept:
- Reject:
- Edit:
- Bury Clone:
- Fingerprint: show fingerprint of the currently-selected clone

### fingerprint window menu

- Quit:
- Help:
- Print: as default

to Table of Contents

last edited: July 1994