eu.isas.peptideshaker.gui.tablemodels

Class ProteinTableModel

java.lang.Object

javax.swing.table.AbstractTableModel

javax.swing.table.DefaultTableModel

com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel

All Implemented Interfaces:

Serializable, TableModel

public class ProteinTableModel
extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

Model for the protein table.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields inherited from class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

isScrolling

Fields inherited from class javax.swing.table.DefaultTableModel

columnIdentifiers, dataVector

Fields inherited from class javax.swing.table.AbstractTableModel

listenerList

Constructor Summary

Constructors

Constructor and Description
ProteinTableModel() Constructor for an empty table
ProteinTableModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, DisplayFeaturesGenerator displayFeaturesGenerator, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, long[] proteinKeys) Constructor.

Method Summary

Modifier and Type	Method and Description
protected void	catchException(Exception e)
Class	getColumnClass(int columnIndex)
int	getColumnCount()
String	getColumnName(int column)
static Integer	getPreferredAccessionColumnWidth(JTable table, int colIndex, int margin, Integer maxProteinKeyLength) Gets the preferred width of the column specified by colIndex.
int	getRowCount()
Object	getValueAt(int row, int column)
boolean	isCellEditable(int rowIndex, int columnIndex)
boolean	isInstantiated() Indicates whether the table content was instantiated.
protected int	loadDataForRows(ArrayList<Integer> rows, com.compomics.util.waiting.WaitingHandler waitingHandler)
void	reset() Reset the protein keys.
static void	setProteinTableProperties(JTable proteinTable, Color sparklineColor, Color sparklineColorNotValidated, Color sparklineColorNotFound, Color sparklineColorDoubtful, DecimalFormat scoreAndConfidenceDecimalFormat, Class parentClass, Integer maxProteinKeyLength) Set up the properties of the protein table.
void	showScores(boolean showScores) Sets whether the scores should be displayed.
void	updateDataModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, DisplayFeaturesGenerator displayFeaturesGenerator, long[] proteinKeys) Update the data in the table model without having to reset the whole table model.

Methods inherited from class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

addScrollListeners, addSortListener, dataMissingAtRow, getRowNumber, getViewIndex, initiateSorter, isScrolling, isSelfUpdating, needsUpdate, resetSorting, setIsScrolling, setSelfUpdating, sort

Methods inherited from class javax.swing.table.DefaultTableModel

addColumn, addColumn, addColumn, addRow, addRow, convertToVector, convertToVector, getDataVector, insertRow, insertRow, moveRow, newDataAvailable, newRowsAdded, removeRow, rowsRemoved, setColumnCount, setColumnIdentifiers, setColumnIdentifiers, setDataVector, setDataVector, setNumRows, setRowCount, setValueAt

Methods inherited from class javax.swing.table.AbstractTableModel

addTableModelListener, findColumn, fireTableCellUpdated, fireTableChanged, fireTableDataChanged, fireTableRowsDeleted, fireTableRowsInserted, fireTableRowsUpdated, fireTableStructureChanged, getListeners, getTableModelListeners, removeTableModelListener

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinTableModel

public ProteinTableModel()

Constructor for an empty table

ProteinTableModel

public ProteinTableModel(com.compomics.util.experiment.identification.Identification identification,
                         com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                         com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                         com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                         com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                         DisplayFeaturesGenerator displayFeaturesGenerator,
                         com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
                         long[] proteinKeys)

Constructor.

Parameters:

identification - the identification containing the protein information

identificationFeaturesGenerator - the identification features generator generating the features of the identification

proteinDetailsProvider - the protein details provider

sequenceProvider - the protein sequences provider

geneMaps - the gene maps

displayFeaturesGenerator - the display features generator generating the display elements

exceptionHandler - an exception handler catching exceptions

proteinKeys - the keys of the protein matches to display

Method Detail

updateDataModel

public void updateDataModel(com.compomics.util.experiment.identification.Identification identification,
                            com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                            com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                            com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                            com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                            DisplayFeaturesGenerator displayFeaturesGenerator,
                            long[] proteinKeys)

Update the data in the table model without having to reset the whole table model. This keeps the sorting order of the table.

Parameters:

identification - the identification containing the protein information

identificationFeaturesGenerator - the identification features generator generating the features of the identification

proteinDetailsProvider - the protein details provider

sequenceProvider - the protein sequences provider

geneMaps - the gene maps

displayFeaturesGenerator - the display features generator generating the display elements

proteinKeys - the keys of the protein matches to display

showScores

public void showScores(boolean showScores)

Sets whether the scores should be displayed.

Parameters:

showScores - a boolean indicating whether the scores should be displayed

reset

public void reset()

Reset the protein keys.

getRowCount

public int getRowCount()

Specified by:

getRowCount in interface TableModel

Overrides:

getRowCount in class DefaultTableModel

getColumnCount

public int getColumnCount()

Specified by:

getColumnCount in interface TableModel

Overrides:

getColumnCount in class DefaultTableModel

getColumnName

public String getColumnName(int column)

Specified by:

getColumnName in interface TableModel

Overrides:

getColumnName in class DefaultTableModel

getValueAt

public Object getValueAt(int row,
                         int column)

Specified by:

getValueAt in interface TableModel

Overrides:

getValueAt in class DefaultTableModel

isInstantiated

public boolean isInstantiated()

Indicates whether the table content was instantiated.

Returns:

a boolean indicating whether the table content was instantiated.

getColumnClass

public Class getColumnClass(int columnIndex)

Specified by:

getColumnClass in interface TableModel

Overrides:

getColumnClass in class AbstractTableModel

isCellEditable

public boolean isCellEditable(int rowIndex,
                              int columnIndex)

Specified by:

isCellEditable in interface TableModel

Overrides:

isCellEditable in class DefaultTableModel

catchException

protected void catchException(Exception e)

Specified by:

catchException in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

loadDataForRows

protected int loadDataForRows(ArrayList<Integer> rows,
                              com.compomics.util.waiting.WaitingHandler waitingHandler)

Specified by:

loadDataForRows in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

setProteinTableProperties

public static void setProteinTableProperties(JTable proteinTable,
                                             Color sparklineColor,
                                             Color sparklineColorNotValidated,
                                             Color sparklineColorNotFound,
                                             Color sparklineColorDoubtful,
                                             DecimalFormat scoreAndConfidenceDecimalFormat,
                                             Class parentClass,
                                             Integer maxProteinKeyLength)

Set up the properties of the protein table.

Parameters:

proteinTable - the protein table

sparklineColor - the sparkline color to use

sparklineColorNotValidated - the sparkline color for not validated stuffs

parentClass - the parent class used to get icons

sparklineColorNotFound - the sparkline color for not found stuffs

sparklineColorDoubtful - the sparkline color for doubtful

scoreAndConfidenceDecimalFormat - the decimal format for score and confidence

maxProteinKeyLength - the longest protein key to display

getPreferredAccessionColumnWidth

public static Integer getPreferredAccessionColumnWidth(JTable table,
                                                       int colIndex,
                                                       int margin,
                                                       Integer maxProteinKeyLength)

Gets the preferred width of the column specified by colIndex. The column will be just wide enough to show the column head and the widest cell in the column. Margin pixels are added to the left and right (resulting in an additional width of 2*margin pixels. Returns null if the max width cannot be set.

Parameters:

table - the table

colIndex - the colum index

margin - the margin to add

maxProteinKeyLength - the maximal protein key length

Returns:

the preferred width of the column