Class IsotopicDistributionPanel

All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible

public class IsotopicDistributionPanel
extends GraphicsPanel
This class provides a JPanel that can display a peptide isotopic distribution.
Version:
$Id$
Author:
Harald Barsnes, Niklaas Colaert, Lennart Martens
See Also:
Serialized Form
  • Constructor Details

    • IsotopicDistributionPanel

      public IsotopicDistributionPanel()
      Empty default constructor
    • IsotopicDistributionPanel

      public IsotopicDistributionPanel​(String peptideSequence, Integer peptideCharge, boolean profileMode, int labelDifference) throws IOException
      This constructor creates an IsotopicDistributionPanel based on the passed parameters.
      Parameters:
      peptideSequence - the peptide sequence to display the isotopic distribution for
      peptideCharge - the charge of the peptide
      profileMode - if true the peaks will be showed in a profile like mode where support peaks are added in front of and after the real peak (note that this is unlike the profile modes of the other graphics panels)
      labelDifference - the number of neutrons to add due to the label
      Throws:
      IOException - if an IOException occurs
  • Method Details

    • addAdditionalDataset

      public void addAdditionalDataset​(String peptideSequence, Integer peptideCharge, Color dataPointAndLineColor, Color areaUnderCurveColor, int labelDifference) throws IOException
      Adds an additional isotopic distribution dataset to be displayed in the same panel. Remember to use different colors for the different datasets.
      Parameters:
      peptideSequence - the peptide sequence to display the isotopic distribution for
      peptideCharge - the charge of the peptide
      dataPointAndLineColor - the color to use for the data points and lines
      areaUnderCurveColor - the color to use for the area under the curve
      labelDifference - the number of neutrons to add due to the label
      Throws:
      IOException - if an IOException occurs
    • isElement

      public boolean isElement​(String lElement)
      Method that checks if a given string is an element we can calculate an isotopic distribution for
      Parameters:
      lElement - String with the element to check
      Returns:
      boolean that indicates if we can use this element
    • getPeptideSequences

      public ArrayList<AASequenceImpl> getPeptideSequences()
      Get the set of peptide sequences.
      Returns:
      the peptideSequences