Added the randomize.features generic and method.
Added calculateOverlapSignificance
The functions need to be tested and finished:
    - sometimes can overlap excluded regions
    - randomized regions are not disjoint
added ymarks and y.at parameters at the heatmapProfile - they regulate the labeling and the positions of the y axis
DESCRIPTION: removed plyr as dependency, still have to figure out if reshape is necessary
R/randomize.feature.R: removed the spurious line from the end of the file
R/scoreMatrixList.R:heatmapProfile: added the functionality to put custom labels and thick marks on th y axis - still have to sort out the margins of the first plot if the labels are too long
inst/tests/GenomationTests.R: added the test for custom y axis for heatmapProfile
R/scoreMatrix.R: added use.names parameter - enables the plotting of the matrix rownames
inst/tests/GenomationTests.R - added intitial tests for the plotMatrix
R/scoreMatrix.R: added the option to remove the separator between the classes
Last commit before branching
Merge branch 'development' of git@github.com:al2na/genomation into devel

Merged comflicts in the description file: plyr added dependency
Merged comflicts in the randomize.feature.R: added automatic chromosome sizecalculation
inst/scripts/FunctionNames.txt: contains the names of the functions that need to be translated into nameName

Conflicts:
	DESCRIPTION
	R/randomize.feature.R
DESCRIPTION:removed second reshape2 dependency
Merge pull request #6 from frenkiboy/development

Development