inst/extdata/
	- added examplary tables

readData.R:
	- working on readGeneric

vignette:
	- working on data read examples
readData.R:
	- changed the position of remove.unusal if statement
readData.R:
	- readGeneric: added the test for the track header

readDataTests.R:
	- started writing tests for readGeneric

inst/tests:
	- added the test files for read generic
readData.R:
	- added the header skipping

readDataTests.R:
	- have to sort out the header skipping
Continued working on the vignette.

Archive was broken.
scoreMatrixList.R:
	- changed all target -> targets

vignette:
	- changed heatmapProfile -> multiHeatMatrix
Sorted out all commits - kept all changes

Merge branch 'development' of github.com:al2na/genomation into development

Conflicts:
	R/readData.R
	R/scoreMatrixList.R
	genomation.Rproj
	inst/tests/readDataTests.R
	inst/tests/tab.test1
	inst/tests/tab.test2
	inst/tests/tab.test3
DESCRIPTION:
	- sorted the whitespace

plotMatrix:
	- removed the ifelse from the arguments and put it into function
	  body

readData:
	- corrected meta.col -> meta.cols in readGeneric

scoreMatrixList.R:
	- changed target->targets
scoreMatrixList.R:
	- changed & -> && when testing for the file
plotMatrix.R:
	- changed GAGE -> CAGE typo

tried to compile the vignette - did not work
Moved the class definition from readAnnotate.R to genomation-classes.R
genomation-classes.R:
	- changed the order of annotationByGenicParts and
	  annotationByFeature

readAnnotate.R:
	- annotateWithFeature: added intersect.chr
NAMESPACE:
	- added plotGeneAnnotation

readAnnotate.R:
	PlotGenicAnnotation
	- plotGenicAnnotation -> plotGeneAnnotation
	- plotGeneAnnotation works
	- added intersect.chr to annotateWithGeneParts
	- changed the GRangeList.obj variable to feature
readAnnotate.R:
	annotateWithFeatureFlank
	- sorted out chr -> chrs
	- feature -> target in intersect.chr=TRUE
	annotateWithFeature
	- sorted out chr -> chrs
	- feature -> target in intersect.chr=TRUE
readAnnotate.R:
genomation-classes.R:
	- changed annotationByGenicParts -> AnnotationByGeneParts
	- changed annotationByFeature -> AnnotationByFeature
NAMESPACE:
	- randomEnrichment -> RandomEnrichment
	- annotationByFeature -> AnnotationByFeature
	- annotationByGeicParts -> AnnotationByGeneParts

genomation-classes.R:
	- randomEnrichment -> RandomEnrichment

getRandomEnrichment.R:
	- randomEnrichment -> RandomEnrichment
	- getRandomEnrichment returned a list not an object
readAnnotate.R:
	- plotGeneAnnotation now works with cluster=TRUE
readAnnotate.R:
	- annotateWithFeature: feature.name taken by default from
	a variable
readAnnotate.R:
	- sorted the whitespace in the function
readAnnotate.R:
	- show:AnnotationByFeature, made the messages more understandable