Graphical results are shown in separate windows. Most functions add their graphical results to a SPIN Sequence Plot that is associated with the sequence being analysed, but some functions such as the restriction enzyme search produce their own separate windows. Each set of graphical results has its own particular default drawing method, but individual results can be "dragged and dropped" by users, hence allowing plots to rearranged and superimposed. Plots can also be extracted from the main graphics window and dropped to create new independent windows. The graphical results can be zoomed and scrolled in both x and y directions. Zooming is achieved using the X and Y scale bars at the bottom of the plot. The individual plots can be scrolled in y using the scroll bars attached to their right hand edge. The sequence can be scrolled using the scroll bar at the base of the plot.
The figure shows a SPIN Sequence Plot containing the results of
a gene search method based on codon usage, upon which is superimposed a
search for start codons and stop codons. The vertical blue line represents
the cursor. The x position of the cursor is shown in the left hand box above
the plot. Each result in the window has its own colour.
At the right hand side of each panel is a set of square boxes with the
same colours as the lines drawn in the adjacent plot. These
icon-like objects represent individual results and allow the user to
operate on them. For example at the right of the middle panel is a
pop-up menu containing the items: "Information", "List results",
"Configure", "Hide" and "Remove".
(
see section Result manager).
The square icons can also be used to move the corresponding results to
new locations. These operations are explained below (
see section Drag and drop).
The cursor in the plot can be used to control the position of the
cursor in the sequence display.
The SPIN Sequence Plot contains three menus: "File", "View" and
"Results". The "File" menu contains the "Exit" command which closes down
the plot; the "View" menu contains the "Results manager" command (
see section Result manager);
and the "Results" menu contains a list of the results, colour coded
i.e. the text is written in the same colour as the plot. For each result
a series of commands can be accessed from a cascading menu.
(
see section Result manager).
Each sequence displayed in a SPIN Sequence Plot will have a corresponding cursor
of a particular colour. The same sequence displayed in several SPIN Sequence Plots
will have a cursor of the same colour. To move a cursor, click on it
with the middle mouse button, or Alt left mouse button,
held down and drag the mouse.
The cursor will move all
other cursors displayed that relate to that sequence, whether these be
in different SPIN Sequence Plots or within the sequence display.
Crosshairs can be turned on or off using the check button labelled
"crosshairs". The x and y positions of the crosshairs are indicated in
the two boxes to the right of the check box respectively. The x value is
the base position in the sequence and the y value the score for the
corresponding plot.
The graphical results can be zoomed and scrolled in both x and y
directions. Zooming is achieved using the X and Y scale bars at the bottom
the plot. The individual plots can be scrolled in y
using the scroll bars attached to their right hand edge. The sequence
can be scrolled using the scroll bar at the base of the plot.
The square boxes at the right edge of the SPIN Sequence Plot panels have the same
colours as the individual results in the display. These icons can be used to
drag and drop the results to which they correspond. This is activated by
pressing the middle mouse button, or Alt left mouse button,
over the box and then moving the cursor
over the SPIN Sequence Plot to the new location. As the cursor moves over each
part of the plot rectangular boxes will appear to indicate the position
that the dragged result will occupy if the mouse button is
released. Results can be dropped on top of another plot (signified by a
rectangle drawn over the centre of the plot), above another plot
(signified by a rectangle drawn in the top third of the plot), or below
another plot (signified by a rectangle drawn in the bottom third of the
plot). The figure below shows three panels containing a protein gene
prediction and three panels showing the positions of stop codons in each
of the reading frames.
The figure below shows the same SPIN Sequence Plot but with the rectangle
indicating where the user has dragged the frame 1 stop codon results.
The figure below shows the result of releasing the middle mouse
button, or Alt left mouse button:
the stop codon plot has moved to be superimposed on the gene
prediction plot.
![[picture]](spin_plot_p.unix.gif.html)
(Click for full size image)
![[picture]](spin_results_manager_d2.unix.gif.html)
(Click for full size image)
Cursors
Crosshairs
Zoom
Drag and drop
![[picture]](spin_plot_drag1.unix.gif.html)
(Click for full size image)
![[picture]](spin_plot_drag2.unix.gif.html)
(Click for full size image)
![[picture]](spin_plot_drag3.unix.gif.html)
(Click for full size image)
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Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/spin_unix_41.html