Class FragmentIonTable

All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, EventListener, Accessible, CellEditorListener, ListSelectionListener, RowSorterListener, TableColumnModelListener, TableModelListener, Scrollable

public class FragmentIonTable
extends JTable
Creates a fragment ion table with the detected fragment ions. Either shows a traditional ion table with the theoretical fragment ions, or a novel version showing the intensities as bar charts for each ion type.
Author:
Harald Barsnes, Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • FragmentIonTable

      public FragmentIonTable()
      Empty default constructor
    • FragmentIonTable

      public FragmentIonTable​(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
      Parameters:
      currentPeptide - the peptide to show the table for
      allAnnotations - the spectrum annotations (from SpectrumAnnotator)
      currentFragmentIonTypes - the list of currently selected fragment ion types
      neutralLosses - the list of the currently selected neutral loss types
      singleCharge - if true, singly charge ions are included in the table
      twoCharges - if true, doubly charged ions are included in the table
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • FragmentIonTable

      public FragmentIonTable​(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, ArrayList<Spectrum> allSpectra, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type. If more than one spectrum annotation set is provided the bars show the average intensities.
      Parameters:
      currentPeptide - the peptide to show the table for
      allAnnotations - the spectrum annotations (from SpectrumAnnotator)
      allSpectra - the list of spectra
      currentFragmentIonTypes - the list of currently selected fragment ion types
      neutralLosses - the list of the currently selected neutral loss types
      singleCharge - if true, singly charge ions are included in the table
      twoCharges - if true, doubly charged ions are included in the table
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
  • Method Details