New Todo Nov 2010
1.  Output HapMap, Plink, Flapjack from alignment.
2.  Add input for Plink and flapjack alignment.
3.  Glazed list for dealing with complex association tables.


Old Migration Notes (still some good ideas):

ToDo:
0.  Make a diagram showing how packages SHOULD be related.  Post to sourceforge. (Terry)
1. Make all tassel projects run on new threads (Terry)
2.  Make a small window below the comment window display to progress for each thread (Terry).
3.  Establish Preferences mechanism (use Java 1.4 mechansim, next generation of Dallas Pref.  Eliminate Settings)(Terry).
4.  Have Results Plugins save their images to file if non-interactive (Ed)
6.  Adapt GLM and MLM to new AnnotationAndCharacterAlignment (Peter, Zhiwu, Ed)
7.  Make GLM, MLM, create kinship matrices into plugins (Peter, Zhiwu)
8.  GDPC Plugin and GDPC Dataloader improve (Terry)
9.  Save Data tree to zip serialization or two text files in same structure.  Make file reader be able to read all the files. (Terry)
10.  Create pipeline to test association for all traits and genes (Terry, Zhiwu)
11.  Create forward mating simulation (Ed)
12.  Add WEKA data miner (Ed).
13.  Pedigree displayer with minimum spanning tree (Terry)
14.  Create pipeline to estimate BLUP values for all traits (Terry, Zhiwu)
15.  Java 6 support much of XML and webservices.  Eliminate redundant libraries (Terry).
18. Remove DataDefinitions (Peter)


Done
3.  Make IdGroupMatrix Interface in PAL, eliminate use of CharacterAlignment were matrices are involved (Ed - Zhiwu)
5.  Remove kinship stuff from GeneralizedAlignmentDistanceMatrix.  Extend it, and make a Kinship matrix class (Ed-Zhiwu).
16. Character alignment class renamings (Terry)
17.  Follow Peter suggestions on revamping Phenotype (Ed)