Package eu.isas.reporter.settings

Class ClusteringSettings

java.lang.Object
eu.isas.reporter.settings.ClusteringSettings
All Implemented Interfaces:
Serializable
public class ClusteringSettings extends Object implements Serializable
Settings for the clustering.
Author:
Marc Vaudel
See Also:

  • Constructor Details

    • ClusteringSettings

      public ClusteringSettings()
      Constructor.

  • Method Details

    • getSelectedProteinClasses

      public ArrayList<String> getSelectedProteinClasses()
      Returns the selected protein cluster classes represented by their toString() method.
      Returns:
      the selected protein cluster classes

    • setSelectedProteinClasses

      public void setSelectedProteinClasses(ArrayList<String> selectedProteinClasses)
      Sets the selected protein cluster classes represented by their toString() method.
      Parameters:
      selectedProteinClasses - the selected protein cluster classes

    • addProteinClass

      public void addProteinClass(String className)
      Adds a class to the selected classes.
      Parameters:
      className - the class name

    • clearProteinClasses

      public void clearProteinClasses()
      Clears the protein classes.

    • getSelectedPeptideClasses

      public ArrayList<String> getSelectedPeptideClasses()
      Returns the selected peptide cluster classes represented by their toString() method.
      Returns:
      the selected peptide cluster classes

    • setSelectedPeptideClasses

      public void setSelectedPeptideClasses(ArrayList<String> selectedPeptideClasses)
      Sets the selected peptide cluster classes represented by their toString() method.
      Parameters:
      selectedPeptideClasses - the selected peptide cluster classes

    • addPeptideClass

      public void addPeptideClass(String className)
      Adds a class to the selected classes.
      Parameters:
      className - the class name

    • clearPeptideClasses

      public void clearPeptideClasses()
      Clears the peptide classes.

    • getSelectedPsmClasses

      public ArrayList<String> getSelectedPsmClasses()
      Returns the selected PSM cluster classes represented by their toString() method.
      Returns:
      the selected PSM cluster classes

    • setSelectedPsmClasses

      public void setSelectedPsmClasses(ArrayList<String> selectedPsmClasses)
      Sets the selected PSM cluster classes represented by their toString() method.
      Parameters:
      selectedPsmClasses - the selected PSM cluster classes

    • addPsmClass

      public void addPsmClass(String className)
      Adds a class to the selected classes.
      Parameters:
      className - the class name

    • clearPsmClasses

      public void clearPsmClasses()
      Clears the peptide classes.

    • getColor

      public Color getColor(String clusterClass)
      Returns the color corresponding to a cluster class.
      Parameters:
      clusterClass - the cluster class
      Returns:
      the corresponding color

    • getNonSelectedColor

      public Color getNonSelectedColor(String clusterClass)
      Returns the color for a non-selected line of this class.
      Parameters:
      clusterClass - the cluster class
      Returns:
      the color for a non-selected line of this class

    • setColor

      public void setColor(String clusterClass, Color color)
      Sets the cluster class color.
      Parameters:
      clusterClass - the cluster class representation as String
      color - the cluster class color

    • getKMeansClusteringSettings

      public com.compomics.util.math.clustering.settings.KMeansClusteringSettings getKMeansClusteringSettings()
      Returns the k-means clustering settings.
      Returns:
      the k-means clustering settings

    • setKMeansClusteringSettings

      public void setKMeansClusteringSettings(com.compomics.util.math.clustering.settings.KMeansClusteringSettings kMeansClusteringSettings)
      Sets the k-means clustering settings.
      Parameters:
      kMeansClusteringSettings - the k-means clustering settings

    • getPossibleProteinClasses

      public ArrayList<String> getPossibleProteinClasses()
      Returns the possible protein classes names.
      Returns:
      the possible protein classes names

    • getProteinClassKey

      public ProteinClusterClassKey getProteinClassKey(String name)
      Returns the class key corresponding to the given name.
      Parameters:
      name - the name
      Returns:
      the class key corresponding to the given name

    • setProteinClassKeys

      public void setProteinClassKeys(ArrayList<ProteinClusterClassKey> clusterClassKeys)
      Sets the cluster class keys.
      Parameters:
      clusterClassKeys - the cluster class keys

    • getProteinKeysMap

      public HashMap<String,ProteinClusterClassKey> getProteinKeysMap()
      Returns a map of the possible keys indexed by their toString() representation.
      Returns:
      a map of the possible keys

    • getPossiblePeptideClasses

      public ArrayList<String> getPossiblePeptideClasses()
      Returns the possible peptide classes names.
      Returns:
      the possible peptide classes names

    • getPeptideClassKey

      public PeptideClusterClassKey getPeptideClassKey(String name)
      Returns the class key corresponding to the given name.
      Parameters:
      name - the name
      Returns:
      the class key corresponding to the given name

    • setPeptideClassKeys

      public void setPeptideClassKeys(ArrayList<PeptideClusterClassKey> clusterClassKeys)
      Sets the cluster class keys.
      Parameters:
      clusterClassKeys - the cluster class keys

    • getPeptideKeysMap

      public HashMap<String,PeptideClusterClassKey> getPeptideKeysMap()
      Returns a map of the possible keys indexed by their toString() representation.
      Returns:
      a map of the possible keys

    • getPossiblePsmClasses

      public ArrayList<String> getPossiblePsmClasses()
      Returns the possible PSM classes names.
      Returns:
      the possible PSM classes names

    • getPsmClassKey

      public PsmClusterClassKey getPsmClassKey(String name)
      Returns the class key corresponding to the given name.
      Parameters:
      name - the name
      Returns:
      the class key corresponding to the given name

    • setPsmClassKeys

      public void setPsmClassKeys(ArrayList<PsmClusterClassKey> clusterClassKeys)
      Sets the cluster class keys.
      Parameters:
      clusterClassKeys - the cluster class keys

    • getPsmKeysMap

      public HashMap<String,PsmClusterClassKey> getPsmKeysMap()
      Returns a map of the possible keys indexed by their toString() representation.
      Returns:
      a map of the possible keys

    • getClassesColors

      public HashMap<String,Color> getClassesColors()
      Returns the classes color coding.
      Returns:
      the classes color coding

    • setClassesColors

      public void setClassesColors(HashMap<String,Color> classesColors)
      Sets the classes color coding.
      Parameters:
      classesColors - the classes color coding