Package eu.isas.reporter.calculation.clustering.keys

Class PeptideClusterClassKey

java.lang.Object
eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey
All Implemented Interfaces:
ClusterClassKey, Serializable
public class PeptideClusterClassKey extends Object implements ClusterClassKey, Serializable
Key for the class of a peptide cluster.
Author:
Marc Vaudel
See Also:

  • Constructor Details

    • PeptideClusterClassKey

      public PeptideClusterClassKey()
      Constructor.

  • Method Details

    • isStarred

      public Boolean isStarred()
      Indicates whether the peptides must be starred.
      Returns:
      a boolean indicating whether the peptides must be starred

    • setStarred

      public void setStarred(Boolean starred)
      Sets whether the peptides must be starred.
      Parameters:
      starred - a boolean indicating whether the peptides must be starred

    • getPossiblePtms

      public ArrayList<String> getPossiblePtms()
      Returns the PTMs possibly carried by the peptides.
      Returns:
      the PTMs possibly carried by the peptides

    • getPossiblePtmsAsSet

      public HashSet<String> getPossiblePtmsAsSet()
      Returns the possible PTMs as a set.
      Returns:
      the possible PTMs as a set

    • setPossiblePtms

      public void setPossiblePtms(ArrayList<String> possiblePtms)
      Sets the PTMs possibly carried by the peptides.
      Parameters:
      possiblePtms - the PTMs possibly carried by the peptides

    • getForbiddenPtms

      public ArrayList<String> getForbiddenPtms()
      Returns the PTMs not carried by the peptide.
      Returns:
      the PTMs not carried by the peptide

    • getForbiddenPtmsAsSet

      public HashSet<String> getForbiddenPtmsAsSet()
      Returns the forbidden PTMs as a set.
      Returns:
      the forbidden PTMs as a set

    • setForbiddenPtms

      public void setForbiddenPtms(ArrayList<String> forbiddenPtms)
      Sets the PTMs not carried by the peptide.
      Parameters:
      forbiddenPtms - the PTMs not carried by the peptide

    • isNotModified

      public boolean isNotModified()
      Indicates whether the peptides must be not modified.
      Returns:
      a boolean indicating whether the peptides must be not modified

    • setNotModified

      public void setNotModified(boolean notModified)
      Sets whether the peptides must be not modified.
      Parameters:
      notModified - a boolean indicating whether the peptides must be not modified

    • isNTerm

      public Boolean isNTerm()
      Indicates whether the peptide is N-term.
      Returns:
      a boolean indicating whether the peptide is N-term

    • setnTerm

      public void setnTerm(Boolean nTerm)
      Sets whether the peptide is N-term.
      Parameters:
      nTerm - a boolean indicating whether the peptide is N-term

    • isCTerm

      public Boolean isCTerm()
      Indicates whether the peptide is C-term.
      Returns:
      a boolean indicating whether the peptide is C-term

    • setcTerm

      public void setcTerm(Boolean cTerm)
      Sets whether the peptide is C-term.
      Parameters:
      cTerm - a boolean indicating whether the peptide is C-term

    • getName

      public String getName()
      Description copied from interface: ClusterClassKey
      Returns the name of the cluster class.
      Specified by:
      getName in interface ClusterClassKey
      Returns:
      the name of the cluster class

    • getDescription

      public String getDescription()
      Description copied from interface: ClusterClassKey
      Returns the description of the cluster class.
      Specified by:
      getDescription in interface ClusterClassKey
      Returns:
      the description of the cluster class

    • toString

      public String toString()
      Overrides:
      toString in class Object