= MatrixModule =

This is the page describing everything surrounding the Matrix module to be developed.
This includes:

 * !MatrixInterface - backend to deal with matrix-like data with implementations for database, file, binary file, plink, and so on. What methods should this interface at least provide?
  * Matrix !LoadDataFromPhenoModel(DB)
 * !MatrixViewer - MOLGENIS user interface plugin to interact with matrices in a useful manner (edit, filter, extract, linkout, annotate, etc)
  * List<Feature> !GetColumnHeaders()
  * List<Target> !GetRowHeaders(!StartRowNr = 0, !EndRowNr = null)
  * !GetValue(Column, Row, Version)
  * !GetValueTimestampStart(Column, Row, Version)
  * !GetValueTimestampEnd(Column, Row, Version)
  * !GetCurrentValueVersion(Column, Row)
  * !SetValue(Column, Row)
  * !SetValueTimestampStart(Column, Row)
  * !SetValueTimestampEnd(Column, Row)
  * !SortOnColumn(!ColumnNr, !StartRowNr = 0, !EndRowNr = null)
  * List<Feature> !RestrictOnEventtype(List<Eventtype>)
  * List<Feature> !RestrictOnFeature(!SearchString)
  * Tuple<Column, Row, Version> Search(!SearchString)
 * !MatrixDisplay - Extensions upon the !MatrixViewer that allow users to make sense of the data like heatmap, pointcloud, network

At the backend, we want a class that loads data from a Pheno OM style data model into a Matrix object. We then want to be able to interact with this Matrix, getting column headers, row headers, and cell values with different versions, each with its own timestamp. In addition, we want to be able to:
 * Sort on columns
 * Restrict the returned row set
 * Restrict the columns (Features), based on
  * A search term
  * One or more Eventtypes of which the Features have to be part. If a Feature is part of more than one Eventtype, the corresponding column should be returned more than once, one time for each Eventtype (true?).
 * Search the Matrix for a specific search string.

Old design

 * MatrixInterface: Interface class with function definitions and all documentation.
 * Matrix: Abstract class with most functions implemented.
 * xxxMatrix: Regular class which is a flavour of Matrix. Functions implemented here work together with the Abstract functions but are specific for this flavour.

{{{
#!graphviz
digraph components
{
MatrixInterface -> Matrix
Matrix -> DatabaseMatrix
Matrix -> BinaryMatrix
Matrix -> FileMatrix
Matrix -> MemoryMatrix
}
}}}

New design:

 * ReadOnlyMatrix: Interface class of the simplest Matrix, so no dependancies and only getter functions.
 * EntityMatrix: Interface class of typed ReadOnlyMatrix, uses org.molgenis.util.Entity to type its rows/colums.
 * EditableMatrix: Interface class of read/writeable Matrix, has add and remove functions for manipulation.
 * MatrixInterface: XGAP specific stuff and complex functions??
 * AbstractMatrix: Other complex functions??
 * AbstractEntityMatrix: Integrates functionality of high level functions with Entities??
 * xxxMatrix: Regular class which is a flavour of Matrix. Functions implemented here work together with the Abstract functions but are specific for this flavour.

Current design in xgap_1_4_distro_hax:
 
{{{
#!graphviz
digraph components
{
ReadonlyMatrix -> EditableMatrix
ReadonlyMatrix -> EntityMatrix
EditableMatrix -> MatrixInterface
ReadonlyMatrix -> AbstractMatrix
AbstractMatrix -> AbstractEntityMatrix
EntityMatrix -> AbstractEntityMatrix
AbstractEntityMatrix -> DatabaseMatrix
AbstractEntityMatrix -> BinaryMatrix
AbstractEntityMatrix -> FileMatrix
AbstractEntityMatrix -> MemoryMatrix
}
}}}



Corrected new design??
 


{{{
#!graphviz
digraph components
{
ReadonlyMatrix -> EditableMatrix
ReadonlyMatrix -> EntityMatrix
EditableMatrix -> MatrixInterface
EntityMatrix -> MatrixInterface
ReadonlyMatrix -> AbstractMatrix
AbstractMatrix -> AbstractEntityMatrix
EntityMatrix -> AbstractEntityMatrix
AbstractEntityMatrix -> DatabaseMatrix
AbstractEntityMatrix -> BinaryMatrix
AbstractEntityMatrix -> FileMatrix
AbstractEntityMatrix -> MemoryMatrix
EditableMatrix -> MemoryMatrix
EditableMatrix -> DatabaseMatrix
MatrixInterface -> DatabaseMatrix
MatrixInterface -> BinaryMatrix
MatrixInterface -> FileMatrix
MatrixInterface -> MemoryMatrix
}
}}}



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