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Nip plot

Graphical results are shown in separate windows. Most functions add their graphical results to a nip plot window 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 top left hand corner 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.

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The figure shows a nip plot window 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 nip plot window 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).

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Cursors

Each sequence displayed in a nip plot will have a corresponding cursor of a particular colour. The same sequence displayed in several nip plots will have a cursor of the same colour. 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 nip 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 x value is the base position in the sequence and the y value the score for the corresponding plot.

Zoom

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 top left hand corner 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.

Drag and drop

The square boxes at the right edge of the nip 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 nip 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.

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The figure below shows the same nip plot but with the rectangle indicating where the user has dragged the frame 1 stop codon results.

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The figure below shows the result of releasing the middle mouse button: the stop codon plot has moved to be superimposed on the gene prediction plot.

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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/nip4_5.html