does rect contain item? rect is the dimensions of the rectangle drawn by a user
with the mouse, and item is any of the 1 or more plot symbols (points, diamonds, etc)
drawn on the surface of the plot.
we start with an array of strings, e.g., {"genetic", "knockout", "bop"}
make this into a single, colon-separated string, for easy comparison with
each experiement's perturbation string, eg, "genetic:knockout:bop"
******
private void oldUpdateRowMap ()
{
ArrayList list = new ArrayList ();
for (int r=0; r < rowState.length; r++) {
if (rowState [r])
list.add (new Integer (r));
} // for r
rowMap = (Integer []) list.toArray (new Integer [0]);
} // oldUpdateRowMap
********
select only those LensedDataMatrices whose structure is identical with the zeroth lens;
congruent matrices have same number of rows and column, same row and column titles
given a perturbationList: {"genetic", "knockout", "boa1", "illumination",
"Dark"} (produced, typically, from a JTree selection, where each of these
strings is a jtree node name on a path create a single colon-separated
string, 'genetic:knockout:boa1:illumination:Dark' then traverse the full
collection of those colon-separated strings, which were read from
'perturbation' predicate of the xml files
this method returns a list of string pairs, in which each pair consists of
the perturbationString (or experimentKey), and a condition.
retrieve an experiment by the value of its perturbation string:
"genetic:knockout:boa1" as specfied in its xml file: these strings are
returned (along with a condition name/value pair) by method
findExperimentKeyForPerturbation, above the perturbationString must be an
exact match to that found in the experiment
This dialog describes the matrices currently loaded into
the MovieController, and makes it possible to edit the node attribute to which
(typically) the data is written.
Find the correlation of all gene expression vectors with the supplied vector
which should be of the same length (i.e., the number of experimental conditions).
return an array of Condition objects
for example, from
string representation of the two resulting condition objects:
[note that no units ("None") are specified for irradiation]
condition: C30, gamma irradiation: false, None, time: 30, minutes
condition: G0 gamma irradiation: true, None time: 0, minutes
if any portion of the subtable specified by the arugments is present in
the target table (currently on top in the browser), then clear any
existing selection and select the intersecting subtable.
I hijack this standard MultipleArrayViewer method, called (perhaps among other places)
from the 'broadcast' button listener I added to org/tigr/microarray/mev/SearchResultDialog.java.
for a 4 row, 3 column matrix:
- swap colums 0 and 2; check the first row
- disable column 0; check the remaining two columns in row 0
- clear the lens; check that the first row equals that of the underlying matrix
test the matrices returned at each of these 3 steps
- get an unmodified view
- select just rows 1 and 2 (implicitly obscuring rows 0 and 3)
- disable first data column
we want "aa:bb:cc"
to match
"aa:bb:cc"
"aa:bb:cc:dd"
"aa:bb:cc:ee"
but not
"aa:bb:ccxxx"
in sampleData/reposTiny we have a legitimate zinc experient xml file
and a ginned up file, to test the above condition.
october 2005: i discovered that (new to java 1.5?) a line with multiple
empty columns, consisting of contiguous tab characters, was parsed with those
empty columns ignored.
Check to see if we can communicate with all currently registered geese
and unregister any that do not respond, then update all geese with the
newly derived list of active geese.