Fixed bug in boolean gate parsing

Boolean gates appearing just below the root were not parsed properly. The code was looking for a parent population that it did not find. Now it checks whether a parent population exists, and whether the parent is a SampleNode.

Signed-off-by: Greg Finak <gfinak@fhcrc.org>
Fixed illegal character escaping when looking for FCS files in the path
quadrant gate name encoding fixed

Signed-off-by: Greg Finak <gfinak@fhcrc.org>
Fixed ellipse fitting
Ellipse fitting.. another bug
Merge branch 'master' of github.com:gfinak/flowWorkspace
ellipse fitting, 1000 nodes in gate for better accuracy

Added optional argument to .ellipseFit, so that the ellipse gate can have an arbitrary number of nodes. Function defaults to 100. Use 1000 in flowWorkspace.

Signed-off-by: Greg Finak <gfinak@fhcrc.org>
version bump for rollout

Signed-off-by: Greg Finak <gfinak@fhcrc.org>
functions to map gates for normalization and some non-essential code removed for speed
fixed check warnings
Fixed check and build errors and exported and documented new functions.

Signed-off-by: Greg Finak <gfinak@fhcrc.org>
reuse plot S4 generic from stats4

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@63449 bc3139a8-67e5-0310-9ffc-ced21a209358
changed flowCore:::colnames to colnames in flowWorkspace2flowCore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@63816 bc3139a8-67e5-0310-9ffc-ced21a209358
comment gc call to improve the speed
merge from remote
merge from remote