Package eu.isas.reporter.gui.tablemodels

Class PsmTableModel

java.lang.Object
javax.swing.table.AbstractTableModel
javax.swing.table.DefaultTableModel
com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
eu.isas.reporter.gui.tablemodels.PsmTableModel
All Implemented Interfaces:
Serializable, TableModel
public class PsmTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Model for the PSM table.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • PsmTableModel

      public PsmTableModel()
      Constructor which sets a new empty table.

    • PsmTableModel

      public PsmTableModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, long[] psmKeys, boolean displayScores, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
      Constructor which sets a new table.
      Parameters:
      identification - the identification object containing the matches
      spectrumProvider - the spectrum provider
      displayFeaturesGenerator - the display features generator
      displayPreferences - the display preferences
      identificationParameters - the identification parameters
      reporterIonQuantification - the reporter quantification information
      quantificationFeaturesGenerator - the quantification feature
      psmKeys - the PSM keys
      displayScores - boolean indicating whether the scores should be displayed instead of the confidence
      exceptionHandler - handler for the exceptions

  • Method Details

    • updateDataModel

      public void updateDataModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, long[] psmKeys, boolean displayScores)
      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
      spectrumProvider - the spectrum provider
      displayFeaturesGenerator - the display features generator
      displayPreferences - the display preferences
      identificationParameters - the identification parameters
      reporterIonQuantification - the reporter quantification information
      quantificationFeaturesGenerator - the quantification feature
      psmKeys - the PSM keys
      displayScores - boolean indicating whether the scores should be displayed instead of the confidence

    • 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