Package com.compomics.util.experiment.identification

Class Advocate

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.Advocate
All Implemented Interfaces:
Serializable
public class Advocate extends ExperimentObject
The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Details

    • mascot

      public static final Advocate mascot
      The Mascot search engine.

    • omssa

      public static final Advocate omssa
      The OMSSA search engine.

    • xtandem

      public static final Advocate xtandem
      The X! Tandem search engine.

    • pepnovo

      public static final Advocate pepnovo
      The PepNovo+ de novo sequencing algorithm.

    • andromeda

      public static final Advocate andromeda
      The Andromeda search engine.

    • msAmanda

      public static final Advocate msAmanda
      The MS Amanda search engine.

    • peptideShaker

      public static final Advocate peptideShaker
      The PeptideShaker multiple algorithm software.

    • msgf

      public static final Advocate msgf
      The MS-GF+ search engine.

    • direcTag

      public static final Advocate direcTag
      The DirecTag sequencing algorithm.

    • byonic

      public static final Advocate byonic
      The Byonic search engine integrated in the Byonic protein metrics interface.

    • comet

      public static final Advocate comet
      The Comet search engine, free version of Sequest.

    • proteinLynx

      public static final Advocate proteinLynx
      The ProteinLynx search engine, waters instruments.

    • msFit

      public static final Advocate msFit
      The MS-Fit search engine, old school peptide mass fingerprinting.

    • myriMatch

      public static final Advocate myriMatch
      The MyriMatch search engine, old school peptide mass fingerprinting.

    • peaks

      public static final Advocate peaks
      The PEAKS sequencing algorithm.

    • phenyx

      public static final Advocate phenyx
      The Phenyx search engine.

    • proFound

      public static final Advocate proFound
      The Profound search engine.

    • proteinProspector

      public static final Advocate proteinProspector
      The search engine results of Protein Prospector.

    • proteinScape

      public static final Advocate proteinScape
      The search engine integrated in Protein Scape, Bruker instruments.

    • sequest

      public static final Advocate sequest
      The Sequest search engine.

    • sqid

      public static final Advocate sqid
      The SeQuence IDentfication (SQID) search engine.

    • scaffold

      public static final Advocate scaffold
      The Scaffold multiple search engine data interpretation software.

    • sonar

      public static final Advocate sonar
      The Sonar search engine, integrated in radars.

    • spectraST

      public static final Advocate spectraST
      The SpectraST spectral library search engine (TPP).

    • spectrumMill

      public static final Advocate spectrumMill
      The Spectrum Mill search engine, Agilent.

    • zCore

      public static final Advocate zCore
      The ZCore search engine, ETD search engine.

    • percolator

      public static final Advocate percolator
      The Percolator rescoring algorithm.

    • pNovo

      public static final Advocate pNovo
      The pNovo+ de novo sequencing algorithm.

    • tide

      public static final Advocate tide
      The Tide search engine.

    • novor

      public static final Advocate novor
      The Novor de novo sequencing algorithm.

    • morpheus

      public static final Advocate morpheus
      The Morpheus search engine.

    • proteinPilot

      public static final Advocate proteinPilot
      The ProteinPilot search engine.

    • onyaseEngine

      public static final Advocate onyaseEngine
      The Onyase engine script.

    • metaMorpheus

      public static final Advocate metaMorpheus
      The MetaMorpheus search engine.

    • identiPy

      public static final Advocate identiPy
      The IdentiPy search engine.

    • coss

      public static final Advocate coss
      The CompOmics Spectral Searching (COSS) engine.

    • sage

      public static final Advocate sage
      The Sage search engine.

    • msFragger

      public static final Advocate msFragger
      The MSFragger search engine.

    • genericMzId

      public static final Advocate genericMzId
      Advocate type for mzId files where no software is annotated.

  • Constructor Details

    • Advocate

      public Advocate()
      Empty default constructor

  • Method Details

    • getIndex

      public int getIndex()
      Returns the index of the advocate.
      Returns:
      the index of the advocate

    • getName

      public String getName()
      Returns the name of the advocate.
      Returns:
      the name of the advocate

    • getType

      public Advocate.AdvocateType getType()
      Returns the type of advocate.
      Returns:
      the type of advocate

    • getColor

      public Color getColor()
      Returns the color of the advocate.
      Returns:
      the color of the advocate

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • values

      public static Advocate[] values()
      Returns the implemented advocates in an array.
      Returns:
      the implemented advocates in an array

    • getAdvocate

      public static Advocate getAdvocate(int index)
      Returns the advocate corresponding to the given index. Null if not found.
      Parameters:
      index - the index of the advocate
      Returns:
      the advocate of interest

    • getAdvocate

      public static Advocate getAdvocate(String advocateName)
      Returns the advocate with the given name. Null if not recognized.
      Parameters:
      advocateName - the name of the advocate of interest
      Returns:
      the advocate with the given name

    • addUserAdvocate

      public static Advocate addUserAdvocate(String advocateName)
      Adds a user advocate and returns it.
      Parameters:
      advocateName - the name of the advocate
      Returns:
      the new advocate

    • getUserAdvocates

      public static HashMap<Integer,Advocate> getUserAdvocates()
      Returns the map of user advocates imported.
      Returns:
      the map of user advocates imported

    • setUserAdvocates

      public static void setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)
      Returns the map of user advocates imported.
      Parameters:
      userAdvocates - the map of user advocates

    • getPmid

      public String getPmid()
      Returns the PubMed id of the reference of the advocate of interest.
      Returns:
      the PubMed id of the reference of the advocate of interest

    • getAdvocateColorMap

      public static HashMap<Integer,Color> getAdvocateColorMap()
      Returns the advocate color map. Key is the advocate index and the element the advocate color.
      Returns:
      the advocate color map

    • getAdvocateToolTipMap

      public static HashMap<Integer,String> getAdvocateToolTipMap()
      Returns the advocate tool tip map. Key is the advocate index and the element the advocate name.
      Returns:
      the advocate tool tip map

    • getAdvocateFromFile

      public static Advocate getAdvocateFromFile(String idFileName)
      Deprecated.
      no longer used
      Returns the advocate based on the identification file name. Null if not found. Note: this method implements a limited number of algorithms and does not support generic files. Use the IdfileReader when possible. Implemented formats: omx > OMSSA dat > Mascot xml > X!Tandem csv > MS-Amanda.
      Parameters:
      idFileName - the name of the identification file
      Returns:
      the advocate likely to have been used to create the given file