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xtree example
Upi Bhalla Mount Sinai June 1995.
This is an example of using the xtree for displaying and manipulating
the hierarchy of GENESIS elements. This mode of use is very similar
to the xtree in the old Xodus, but there are many more facilities.
RUNNING:
cd into this directory
start GENESIS
type tree
You will see a window with lots of funny looking icons. (Some of these
will be out of view, to the right. Remember that you may pan the draw
window by using the cursor arrow keys.)
- The triangles represent neutrals
- The cylinders represent compartments
- The funny shapes that look like a voltage gated channels are
voltage gated channels. This won't be much help unless you already
know what a voltage gated channel looks like.
- The christmas-tree like object represents an xtree
- Anything which the xtree has no explicit icon for is represented
by a rectangle. This includes the tables
- The arrows represent messages
THINGS TO DO:
1. Click on any icon. The name of the element should
be printed in the genesis console.
2. Double-click on an icon which has children. The children will
vanish and the icon will now be 'stacked' to indicate that
it has children but they are shy.
3. Double click on the icon again. The children will reappear.
4. Look at the hierarchy of the /cell element on the xtree.
It is a flat hierarchy, which is the convention. In other words,
all compartments are children of the /cell element. Verify this
by doing
le /cell
5. Let us change this to a hierarchy based on the tree structure of
the cell itself. Click on dend1 and drag it onto the soma.
Poof ! The tree changes to reflect this new hierarchy.
Do
le /cell/soma
to verify that the same change was done to the genesis element
hierarchy.
6. Lets change the hierarchy from the command line. Do
move /cell/dend2 /cell/soma
from the command line. Funny. Nothing happens. This is because the
xtree has not been told about the change. You can force an update
in two ways:
- Double click on the cell, twice. The clicks force an update.
- Call the RESET action for the tree:
call /form/draw/tree RESET
7. Some strange people believe that a tree should grow upside down,
with the root on top and the leaves below. I have found it
is much easier to give them what they want, rather than argue
with such people. To allay whatever childhood trauma they underwent
from the fact that the leaves of the tree are at the top (and
hence a longer fall to the ground), you can turn the tree upside
down:
setfield /form/draw/tree orientation down
call /form/draw/tree RESET
setfield /form/draw ymin -6
For the severely emotionally stricken, you can even turn the tree
on its side:
setfield /form/draw/tree orientation left
call /form/draw/tree RESET
setfield /form/draw/tree orientation right
call /form/draw/tree RESET
of course, you may have to adjust the dimensions of the draw
window to be able to see the tree in this configuration.
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