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Sip plot

The sip plot display shows the results of comparison algorithms. Each match is represented as either a single dot ("find similar spans", "find best diagonals") or a line ("find matching words", "align sequences"). Sets of matches from a single invocation of a comparison command are termed "a result". Each result is plotted using a single colour which can be configured via the results manager ( see section Result manager). The maximum dimensions of the sip plot are indicated on the rulers at the bottom and left hand side. It is possible within SIP to compare many different sequences. This means that there may be more than one horizontal or vertical sequence shown in the sip plot. All the points are scaled to the largest sequence in each direction. Plots can also be extracted from or added to each sip plot.

[picture]

The diagram above shows the results of a "find similar spans" search (olive) ( see section Find similar spans), and a "find matching words" (red) ( see section Find matching words), between human and mouse properdin (hsproperd and mmproper). For those viewing in black and white they are black. At the right hand side is a set of square boxes with the same colours as the dots drawn in the adjacent plot. These icon-like objects represent individual results and allow the user to operate on them. For example the pop-up menu beneath the "matching words" result contains the results menu for this result ( 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 sip plot has 3 menus, "File", "View" and "Results".

The "File" menu contains the "Exit" command to quit the sip plot. This shuts down the sip plot display removes all the results displayed in that plot.

The "View" menu contains the "Results manager" command, see section Result manager.

The "Results" menu provides a quick method of interfacing with the menu obtainable via the "Results manager" ( see section Result manager).

Cursors

Each sequence displayed in a sip plot will have a corresponding cursor of a particular colour. In the picture above, the sequence on the horizontal axis has a vertical blue cursor whereas the sequence on the vertical axis has a horizontal olive green cursor. The same sequence displayed in several sip plots will have a cursor of the same colour unless the sequence has been plotted on a different axis. The x and y positions of the cursors are indicated in the two boxes to the right of the crosshair check box respectively. To move a cursor, click on it with the middle 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 sip plots, the sequence display or even in different programs if the sequence has been sent to or been received from another program. (See section Inter-program communication.)

Crosshairs

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 position of the crosshairs can be "frozen" at a particular position by pressing the control button and moving the mouse cursor outside the sip plot window.

Zoom

Plots can be enlarged either by resizing the window or zooming. Zooming is achieved by holding down the control key and right mouse button and dragging out a rectangle. Rectangles that are too small are ignored and a warning bell will sound. The Back button will restore the plot to the previous magnification. Zooming will increase the magnification of the plot so that the contents of the dragged out rectangle fill the display. The scrollbars allow the sip plot to be scrolled in both directions.

It is not possible to zoom on temporary results.

Drag and drop

The square boxes at the right edge of the sip 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 over the box and then moving the cursor over the sip plot to the new location or anywhere outside the sip plot. 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). Moving the mouse cursor outside the sip plot and releasing the mouse button will create a new sip plot containing that result.


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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/sip_2.html