eu.isas.peptideshaker.gui.tablemodels

Class PsmTableModel

java.lang.Object

javax.swing.table.AbstractTableModel

javax.swing.table.DefaultTableModel

com.compomics.util.gui.tablemodels.SelfUpdatingTableModel

eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

All Implemented Interfaces:

Serializable, TableModel

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

Table model for a set of peptide to spectrum matches.

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
PsmTableModel() Constructor for an empty table.
PsmTableModel(com.compomics.util.experiment.identification.Identification identification, DisplayFeaturesGenerator displayFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] psmKeys, boolean displayScores, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor which sets a new table.

Method Summary

Modifier and Type	Method and Description
protected void	catchException(Exception e)
Class	getColumnClass(int columnIndex)
int	getColumnCount()
String	getColumnName(int column)
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() Resets the peptide keys.
void	showScores(boolean showScores) Sets whether the scores should be displayed.
void	updateDataModel(com.compomics.util.experiment.identification.Identification identification, DisplayFeaturesGenerator displayFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] psmKeys) 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

PsmTableModel

public PsmTableModel()

Constructor for an empty table.

PsmTableModel

public PsmTableModel(com.compomics.util.experiment.identification.Identification identification,
                     DisplayFeaturesGenerator displayFeaturesGenerator,
                     com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                     com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                     long[] psmKeys,
                     boolean displayScores,
                     com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Constructor which sets a new table.

Parameters:

identification - the identification object containing the matches

displayFeaturesGenerator - the display features generator

spectrumProvider - The spectrum provider.

identificationParameters - the identification parameters

psmKeys - the PSM keys

displayScores - boolean indicating whether the scores should be displayed instead of the confidence

exceptionHandler - handler for the exceptions

Method Detail

updateDataModel

public void updateDataModel(com.compomics.util.experiment.identification.Identification identification,
                            DisplayFeaturesGenerator displayFeaturesGenerator,
                            com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                            long[] psmKeys)

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 object containing the matches

displayFeaturesGenerator - the display features generator

identificationParameters - the identification parameters

psmKeys - the PSM keys

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()

Resets the peptide 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