phenote.matrix.model
Class MatrixController

java.lang.Object
  phenote.matrix.model.MatrixController

public class MatrixController
extends java.lang.Object

Constructor Summary

MatrixController()
Creates a new matrix controller

Method Summary

void	buildColumns() Traverses the character list and extracts the entity, quality, and additional entity from each one.
void	buildMatrix() Gets the current list of characters and calls methods to build the rows and columns of the matrix
void	buildRows() Traverses the character list and extracts the valid taxon from each one.
java.lang.String	getColumnHeader(int index)
java.util.ArrayList<MatrixColumn>	getColumns()
int	getNumColumns()
int	getNumRows()
java.util.ArrayList<MatrixRow>	getRows()
java.lang.Object	getValueAt(int rowIndex, int colIndex) This method iterates through each character in the main data list and checks to see if it is a valid character for the given row and given column in the matrix.
void	initializeVars() Creates new instances of all instance variables

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MatrixController

public MatrixController()

Creates a new matrix controller

Method Detail

initializeVars

public void initializeVars()

Creates new instances of all instance variables

buildMatrix

public void buildMatrix()
                 throws CharFieldException

Gets the current list of characters and calls methods to build the rows and columns of the matrix

Throws:

CharFieldException

buildRows

public void buildRows()

Traverses the character list and extracts the valid taxon from each one. Each taxon is made into a PhenotypeMatrixRow object, and that object is put into a Set, assuring that there will be no duplicates. Once the set is complete, each element of the set is added to an ArrayList. (This was done to maintain compatibility with other parts of the code that expected the rows to be stored in an ArrayList; it probably could be refactored to use the Set and eliminate the ArrayList entirely.)

buildColumns

public void buildColumns()

Traverses the character list and extracts the entity, quality, and additional entity from each one. The resulting tuple is made into a PhenotypeMatrixColumn object, and that object is put into a Set, assuring that there will be no duplicates. Once the set is complete, each element of the set is added to an ArrayList. (This was done to maintain compatibility with other parts of the code that expected the columns to be stored in an ArrayList; it probably could be refactored to use the Set and eliminate the ArrayList entirely.)

getValueAt

public java.lang.Object getValueAt(int rowIndex,
                                   int colIndex)

This method iterates through each character in the main data list and checks to see if it is a valid character for the given row and given column in the matrix. Once it finds a match, it uses the getValue() method from PhenotypeMatrixColumn class to create a new PhenotypeMatrixCell object, and returns it.

Parameters:

rowIndex - the number of the row being requested

colIndex - the number of the column being requested

Returns:

an Object (actually the PhenotypeMatrixCell) representing the contents of the matrix at the requested location

getColumnHeader

public java.lang.String getColumnHeader(int index)

Parameters:

index - the index of the column whose header is being requested

Returns:

a String representing the name of the requested column

getNumRows

public int getNumRows()

Returns:

the number of rows in the current matrix

getNumColumns

public int getNumColumns()

Returns:

the number of columns in the current matrix

getRows

public java.util.ArrayList<MatrixRow> getRows()

Returns:

an ArrayList describing the rows of the matrix

getColumns

public java.util.ArrayList<MatrixColumn> getColumns()

Returns:

an ArrayList describing the columns of the matrix