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
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last edited: July 1994