choose index on random

git-svn-id: http://beast-mcmc.googlecode.com/svn@6627 ca793f91-a31e-0410-b540-2769d408b6a1
Operator in disguise

git-svn-id: http://beast-mcmc.googlecode.com/svn@6628 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed Issue 749:	Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction

git-svn-id: http://beast-mcmc.googlecode.com/svn@6629 ca793f91-a31e-0410-b540-2769d408b6a1
Caching gives a 10-fold speed up over not-caching.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6630 ca793f91-a31e-0410-b540-2769d408b6a1
Cleaning up a bit.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6631 ca793f91-a31e-0410-b540-2769d408b6a1
Preventing updateLocation being called more than once per step if caching is on.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6632 ca793f91-a31e-0410-b540-2769d408b6a1
Unrolled the cache array - didn't improve things much. Still copying way to much data.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6633 ca793f91-a31e-0410-b540-2769d408b6a1
Created a new caching version of MDSC. Much faster (another order of magnitude) however, deviates from the non cached version after 800 steps (not clear why just yet).

git-svn-id: http://beast-mcmc.googlecode.com/svn@6634 ca793f91-a31e-0410-b540-2769d408b6a1
commiting to get the build

git-svn-id: http://beast-mcmc.googlecode.com/svn@6635 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed a bug where scaling the data could sometimes cause the chain to be stuck

git-svn-id: http://beast-mcmc.googlecode.com/svn@6636 ca793f91-a31e-0410-b540-2769d408b6a1
Linking up native MDS.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6637 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed a short array copy.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6638 ca793f91-a31e-0410-b540-2769d408b6a1
Move Math.log(double) from C++ back to Java to match bit-stream in MDS

git-svn-id: http://beast-mcmc.googlecode.com/svn@6639 ca793f91-a31e-0410-b540-2769d408b6a1
First implementation of M-H step. Not tested.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6640 ca793f91-a31e-0410-b540-2769d408b6a1
Implements GaussianProcessFromTree.
Removes caching from LFM

git-svn-id: http://beast-mcmc.googlecode.com/svn@6641 ca793f91-a31e-0410-b540-2769d408b6a1
missing imports

git-svn-id: http://beast-mcmc.googlecode.com/svn@6642 ca793f91-a31e-0410-b540-2769d408b6a1
streamlined version for debugging

git-svn-id: http://beast-mcmc.googlecode.com/svn@6643 ca793f91-a31e-0410-b540-2769d408b6a1
dirty but works

git-svn-id: http://beast-mcmc.googlecode.com/svn@6644 ca793f91-a31e-0410-b540-2769d408b6a1
Restored exit(0) at end of main().

git-svn-id: http://beast-mcmc.googlecode.com/svn@6645 ca793f91-a31e-0410-b540-2769d408b6a1
Can't cast an object to a double (cast to Double and then unbox).

git-svn-id: http://beast-mcmc.googlecode.com/svn@6646 ca793f91-a31e-0410-b540-2769d408b6a1