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