|
| |
A further description of Pairwise Comparative Map (PCM)
is given below and it's main functions are highlighted.
 | The Maps. |
When a PCM component is fed a PCM file or set of native Java data
objects, (see Data section), either one or two genetic
maps are drawn. These can be any sort of linear genetic map, (e.g. linkage,
physical, introgression). If two maps are drawn, lines link the homologous loci on either
map. If a locus has no homologous loci on the other side, no connecting lines get drawn.
It is possible for a locus to have a homologue on the same map but no line will be drawn
between them.
| Highlighting |
Clicking on a locus highlights it in red along with any homologous
loci on the same map and on the opposite map. All linking lines are also highlighted in
red. Double-clicking the locus retrieves the URL to the datum object (if one has been
entered in the PCM file). If the component is running within an applet, a web browser can
be fired up with this URL (but the programmer implementing the bioWidget has to set this up themselves).
| Button Bar.
A number of buttons are found at the bottom of the map
like shown in the image below:
 | Clicking on Swap swaps the map on the LHS
for the map on the RHS, vice-versa.
|
| Clicking on Invert1 or Invert2
inverts the appropriate map, i.e. instead of running from 0 to n from
top to bottom, the map runs from n to 0. You can see an example of an inverted PCM.
|
| Clicking on Resize1 or Resize2
produces a dialogue box like the following one:
|
|
The user can adjust the pixel length of the map from
the value shown to the desired value using the scrollbar or the number input box. To use
the later, type an integer in to the box and press return. The number will appear above
the box in red.
Each map can be stretched out to a great length as the
component only paints what is actually on the screen (rather than the whole map). The
scale bar will not resolve to steps of less than 1.0- it stretches out the distance
between ticks on the scale bar instead if necessary.
| Sausage Colour.
The green bars that represent the chromosomes are
called sausages. If the data sets that make up the maps originate from different
databases these are given different colours. For example if the map on the LHS comes from
an Arabidopsis database, the sausage might be coloured green and if the map on the RHS
comes from Brassicas, the sausage might be coloured yellow. It is therefore immediately
apparent that these data sets originate from different databases and are possibly from
different species.
The default sausage colours are green and yellow but
these can be customised easily by a programmer who is implementing the Java Bean in an integrated development environment, (IDE).
|
| Multi PCM.
There is a higher level component to PCM which
is part of the same package called Multi PCM. This consists of a number of PCMs sitting
adjacent to one another in a scrollpane and one can scroll along the pane and view the
different maps. (An image of this is given here). If
one highlights a locus, all loci with the same name (and their homologues) are highlighted
across all the maps. In addition all the sausages of all the maps that originate from the
same databases are coloured the same, i.e. all Arabidopsis maps might be green,
all Lolium maps might be yellow and all Brassicas maps might be orange.
|
| IDE Java Bean
support.
|
PCM is written as a Java Bean and has a Bean Info
class. This means that it can be used graphically in a Java Integrated Development
Environment. This allows the component to be used in a drag and drop fashion so that
the user has to write an absolute minimum of code. It also allows you to easily modify
some variables very easily such as the start-up length of the LHS and RHS sausages and the
colour the sausages should be coloured. See the IDE guide
of the Programmers section.
 
ŠJeremy Dickson, October 1998.
|
