Changed all colt dependecies in systemsgenetics to parallelcolt

Colt 1.2.0 and Colt1.0.3 are dependencies of dependecies of other
libraries so are still in after downloading. Try to use the parallelcolt
functions when possible.
SNP necessary for PCopt
introduction of matrix.DoubleMatrixDataset

Moved DoubleMatrixDataset2 to legacy. Before definitive removal.
Merge pull request #30 from Bonder-MJ/master

SNP lists necessary for PCopt, Changed to parallelcolt, new double matrix
DoubleMatrixDataset extends DoubleMatrix2D allowing it to be used by lots of COLT functions
Merge pull request #31 from PatrickDeelen/master

DoubleMatrixDataset extends DoubleMatrix2D allowing it to be used by lots of COLT functions
Fixed transpose issues. No works same as other colt matrix using viewDice. This will create an view (not a copy) of the orignal dataset that refects modifications of the original. This is the same behaivor of viewDice in other colt matrix implementations
removed old get row count since this is already present when extending double matrix from colt
Please check these two functions: setNrRows and setNrCols. I think they are invalid
Merge pull request #32 from PatrickDeelen/master

Fixed some issues with double matrix
Bug fix transpose smallDoubleMatrix. Copy paste is evil
Merge pull request #33 from PatrickDeelen/master

Bug fix transpose smallDoubleMatrix. Copy paste is evil
Working on T stat matrix from illumina
Merge branch 'master' of github.com:molgenis/systemsgenetics