development branch first commit
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
automatic chromosome size extraction as furthest point
Description changed, readme added
new refseq.bed file and problem with ifelse from R 3.0.2 is fixed. ifelse() function was not working as it used to work. Now it is fixed. also ifelse() functions replaced with if()else() control structures. thanks for that annoyance R.
examples for read.transcript.features are added
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
Merge branch 'development' of git@github.com:al2na/genomation into development

Pulled the development branch after I messed up and deleted the whole project folder.

Conflicts:
	DESCRIPTION
	R/scoreMatrixList.R
Renamed 2 files, and changed the DESCRIPTION accordingly.
Changed all the function names to correspond to the Bioconductor standard.
Faux commit of the DESCRIPTION file - nothing changed
Merge pull request #7 from frenkiboy/development

Development
Corrected the function names in the NAMESPACE file
Merge pull request #8 from frenkiboy/development

Corrected the function names in the NAMESPACE file