baseCode

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## Todos

Class | Class Todos Count | Method with Todos
--- | --- | ---
baseCode.bio.geneset.GONames | 0 | 2
baseCode.common.Distanceable | 0 | 1
baseCode.dataFilter.RowAbsentFilter | 0 | 1
baseCode.dataStructure.graph.DirectedGraph | 1 | 1
baseCode.gui.JMatrixDisplay | 0 | 1
baseCode.gui.TreePanel | 1 | 0
baseCode.gui.WizardStep | 0 | 1
baseCode.math.MatrixRowStats | 1 | 1
baseCode.math.MatrixStats | 0 | 1
baseCode.math.Stats | 0 | 1

### baseCode.bio.geneset.GONames

Method Todos
addClass(): this should modify the tree representation too.

Method Todos
modifyClass(): this should modify the tree representation too.

### baseCode.common.Distanceable

Method Todos
toCollection(): not very elegant...

### baseCode.dataFilter.RowAbsentFilter

Method Todos
validateFlags(): this should check more carefully - actually test that the rows are all the same.

### baseCode.dataStructure.graph.DirectedGraph

Class Todos
do something about cyclicity; make this a dag or a subclass...

Method Todos
treeView(): note that nodes are only allowed to have one parent in DefaultMutableTreeNodes

### baseCode.gui.JMatrixDisplay

Method Todos
saveImage(): never read

### baseCode.gui.TreePanel

Class Todos
- this really doesn't do much.

### baseCode.gui.WizardStep

Method Todos
addHelp(): why the spaces for layout?

### baseCode.math.MatrixRowStats

Class Todos
Have min() and max() throw an EmptyMatrixException -- this exception class does not yet exist and needs to be defined somewhere.

Method Todos
sums(): calls new a lot.

### baseCode.math.MatrixStats

Method Todos
correlationMatrix(): this is pretty inefficient - calls new

### baseCode.math.Stats

Method Todos
cv(): offer a regularized version of this function.