Package eu.isas.peptideshaker.preferences

Class ProjectDetails

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
eu.isas.peptideshaker.preferences.ProjectDetails
All Implemented Interfaces:
Serializable
public class ProjectDetails extends com.compomics.util.experiment.personalization.ExperimentObject
This class contains the details about a project.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • ProjectDetails

      public ProjectDetails()
      Constructor.

  • Method Details

    • getIdentificationFiles

      public ArrayList<String> getIdentificationFiles()
      Getter for all identification files loaded.
      Returns:
      all identification files loaded

    • addIdentificationFiles

      public void addIdentificationFiles(File identificationFile)
      Adds an identification file to the list of loaded identification files.
      Parameters:
      identificationFile - the identification file loaded

    • addSpectrumFilePath

      public void addSpectrumFilePath(String spectrumFilePath)
      Attaches a spectrum file to the project.
      Parameters:
      spectrumFilePath - the spectrum file to add

    • getSpectrumFileNames

      public Set<String> getSpectrumFileNames()
      Returns the name of the input spectrum files as a set.
      Returns:
      the spectrum file names

    • getSpectrumFilePath

      public String getSpectrumFilePath(String fileName)
      Returns the path to the file corresponding to the given name. Null if not found.
      Parameters:
      fileName - the name without extension of the desired file
      Returns:
      the corresponding file, null if not found.

    • setFastaFile

      public void setFastaFile(File fastaFile)
      Set the path to the FASTA file.
      Parameters:
      fastaFile - the FASTA file

    • getFastaFile

      public String getFastaFile()
      Returns the path to the FASTA file.
      Returns:
      the path to the FASTA file

    • getCreationDate

      public Date getCreationDate()
      Getter for the creation date of the project.
      Returns:
      the creation date of the project

    • setCreationDate

      public void setCreationDate(Date creationDate)
      Setter the creation date of the project.
      Parameters:
      creationDate - the creation date of the project

    • getPeptideShakerVersion

      public String getPeptideShakerVersion()
      Returns the PeptideShaker version used to create the project.
      Returns:
      the PeptideShaker version used to create the project

    • setPeptideShakerVersion

      public void setPeptideShakerVersion(String peptideShakerVersion)
      Sets the PeptideShaker version used to create the project.
      Parameters:
      peptideShakerVersion - the PeptideShaker version used to create the project

    • getReport

      public String getReport()
      Returns the report created during the loading of the project.
      Returns:
      the report created during the loading of the project

    • setReport

      public void setReport(String report)
      Set the report created during the loading of the project.
      Parameters:
      report - the report to set

    • getPrideExperimentTitle

      public String getPrideExperimentTitle()
      Returns the PRIDE experiment title.
      Returns:
      the prideExperimenttitle

    • setPrideExperimentTitle

      public void setPrideExperimentTitle(String prideExperimentTitle)
      Sets the PRIDE experiment title.
      Parameters:
      prideExperimentTitle - the prideExperimentTitle to set

    • getPrideExperimentLabel

      public String getPrideExperimentLabel()
      Returns the PRIDE experiment label.
      Returns:
      the prideExperimentLabel

    • setPrideExperimentLabel

      public void setPrideExperimentLabel(String prideExperimentLabel)
      Sets the PRIDE experiment label.
      Parameters:
      prideExperimentLabel - the prideExperimentLabel to set

    • getPrideExperimentProjectTitle

      public String getPrideExperimentProjectTitle()
      Returns the PRIDE experiment project title.
      Returns:
      the prideExperimentProjectTitle

    • setPrideExperimentProjectTitle

      public void setPrideExperimentProjectTitle(String prideExperimentProjectTitle)
      Set the PRIDE experiment project title.
      Parameters:
      prideExperimentProjectTitle - the prideExperimentProjectTitle to set

    • getPrideExperimentDescription

      public String getPrideExperimentDescription()
      Returns the PRIDE experiment project description.
      Returns:
      the prideExperimentDescription

    • setPrideExperimentDescription

      public void setPrideExperimentDescription(String prideExperimentDescription)
      Set the PRIDE experiment project description.
      Parameters:
      prideExperimentDescription - the prideExperimentDescription to set

    • getPrideReferenceGroup

      public com.compomics.util.pride.prideobjects.ReferenceGroup getPrideReferenceGroup()
      Returns the PRIDE reference group.
      Returns:
      the prideReferenceGroup

    • setPrideReferenceGroup

      public void setPrideReferenceGroup(com.compomics.util.pride.prideobjects.ReferenceGroup prideReferenceGroup)
      Set the PRIDE reference group.
      Parameters:
      prideReferenceGroup - the prideReferenceGroup to set

    • getPrideContactGroup

      public com.compomics.util.pride.prideobjects.ContactGroup getPrideContactGroup()
      Returns the PRIDE contact group.
      Returns:
      the prideContactGroup

    • setPrideContactGroup

      public void setPrideContactGroup(com.compomics.util.pride.prideobjects.ContactGroup prideContactGroup)
      Set the PRIDE contact group.
      Parameters:
      prideContactGroup - the prideContactGroup to set

    • getPrideSample

      public com.compomics.util.pride.prideobjects.Sample getPrideSample()
      Returns the PRIDE sample.
      Returns:
      the prideSample

    • setPrideSample

      public void setPrideSample(com.compomics.util.pride.prideobjects.Sample prideSample)
      Set the PRIDE sample.
      Parameters:
      prideSample - the prideSample to set

    • getPrideProtocol

      public com.compomics.util.pride.prideobjects.Protocol getPrideProtocol()
      Returns the PRIDE protocol.
      Returns:
      the prideProtocol

    • setPrideProtocol

      public void setPrideProtocol(com.compomics.util.pride.prideobjects.Protocol prideProtocol)
      Set the PRIDE protocol.
      Parameters:
      prideProtocol - the prideProtocol to set

    • getPrideInstrument

      public com.compomics.util.pride.prideobjects.Instrument getPrideInstrument()
      Returns the PRIDE instrument.
      Returns:
      the prideInstrument

    • setPrideInstrument

      public void setPrideInstrument(com.compomics.util.pride.prideobjects.Instrument prideInstrument)
      Set the the PRIDE instrument.
      Parameters:
      prideInstrument - the prideInstrument to set

    • getPrideOutputFolder

      public String getPrideOutputFolder()
      Returns the PRIDE output folder.
      Returns:
      the prideOutputFolder

    • setPrideOutputFolder

      public void setPrideOutputFolder(String prideOutputFolder)
      Set the PRIDE output folder.
      Parameters:
      prideOutputFolder - the prideOutputFolder to set

    • getMzIdentMLOutputFile

      public String getMzIdentMLOutputFile()
      Returns the mzIdentML output file.
      Returns:
      the mzIdentML output file

    • setMzIdentOutputFile

      public void setMzIdentOutputFile(String mzIdentMLOutputFile)
      Set the mzIdentML output file.
      Parameters:
      mzIdentMLOutputFile - the mzIdentMLOutputFile to set

    • hasIdentificationAlgorithms

      public boolean hasIdentificationAlgorithms()
      Returns true if the identification algorithms are stored.
      Returns:
      true if the identification algorithms are stored

    • getIdentificationAlgorithms

      public ArrayList<Integer> getIdentificationAlgorithms()
      Returns a list of identification algorithms used based on the identification files of the project.
      Returns:
      a list of identification algorithms indexed by the static field of the Advocate class

    • getAlgorithmNameToVersionsMap

      public HashMap<String,ArrayList<String>> getAlgorithmNameToVersionsMap()
      Returns the different identification algorithm versions used in a map: algorithm name > versions.
      Returns:
      the different identification algorithm versions used

    • getIdentificationAlgorithmsForFile

      public HashMap<String,ArrayList<String>> getIdentificationAlgorithmsForFile(String idFileName)
      Returns the identification algorithms used to create the id file in map: algorithm name > algorithm version.
      Parameters:
      idFileName - the identification file name
      Returns:
      the identification algorithms used

    • setIdentificationAlgorithmsForFile

      public void setIdentificationAlgorithmsForFile(String idFileName, HashMap<String,ArrayList<String>> fileIdentificationAlgorithms)
      Sets the identification algorithms used to create an identification file.
      Parameters:
      idFileName - the name of the identification file
      fileIdentificationAlgorithms - the identification algorithms used to create this file in a map: algorithm name > versions

    • getContactFirstName

      public String getContactFirstName()
      Returns the first name of the contact for the mzIdentML dataset.
      Returns:
      the contactFirstName

    • setContactFirstName

      public void setContactFirstName(String contactFirstName)
      Set the first name of the contact for the mzIdentML dataset.
      Parameters:
      contactFirstName - the contactFirstName to set

    • getContactLastName

      public String getContactLastName()
      Returns the last name of the contact for the mzIdentML dataset.
      Returns:
      the contactLastName

    • setContactLastName

      public void setContactLastName(String contactLastName)
      Set the last name of the contact for the mzIdentML dataset.
      Parameters:
      contactLastName - the contactLastName to set

    • getContactEmail

      public String getContactEmail()
      Returns the e-mail of the contact for the mzIdentML dataset.
      Returns:
      the contactEmailName

    • setContactEmail

      public void setContactEmail(String contactEmail)
      Set the e-mail of the contact for the mzIdentML dataset.
      Parameters:
      contactEmail - the contactEmailName to set

    • getContactUrl

      public String getContactUrl()
      Returns the URL of the contact for the mzIdentML dataset.
      Returns:
      the contactUrl

    • setContactUrl

      public void setContactUrl(String contactUrl)
      Set the first URL of the contact for the mzIdentML dataset.
      Parameters:
      contactUrl - the contactUrl to set

    • getContactAddress

      public String getContactAddress()
      Returns the address of the contact for the mzIdentML dataset.
      Returns:
      the contactAddress

    • setContactAddress

      public void setContactAddress(String contactAddress)
      SEt the address of the contact for the mzIdentML dataset.
      Parameters:
      contactAddress - the contactAddress to set

    • getOrganizationName

      public String getOrganizationName()
      Returns the name of the organization for the mzIdentML dataset.
      Returns:
      the organizationName

    • setOrganizationName

      public void setOrganizationName(String organizationName)
      Set the name of the organization for the mzIdentML dataset.
      Parameters:
      organizationName - the organizationName to set

    • getOrganizationEmail

      public String getOrganizationEmail()
      Returns the e-mail of the organization for the mzIdentML dataset.
      Returns:
      the organizationEmail

    • setOrganizationEmail

      public void setOrganizationEmail(String organizationEmail)
      Set the name of the organization for the mzIdentML dataset.
      Parameters:
      organizationEmail - the organizationEmail to set

    • getOrganizationUrl

      public String getOrganizationUrl()
      Returns the URL of the organization for the mzIdentML dataset.
      Returns:
      the organizationUrl

    • setOrganizationUrl

      public void setOrganizationUrl(String organizationUrl)
      Set the URL of the organization for the mzIdentML dataset.
      Parameters:
      organizationUrl - the organizationUrl to set

    • getOrganizationAddress

      public String getOrganizationAddress()
      Returns the address of the organization for the mzIdentML dataset.
      Returns:
      the organizationAddress

    • setOrganizationAddress

      public void setOrganizationAddress(String organizationAddress)
      Set the address of the organization for the mzIdentML dataset.
      Parameters:
      organizationAddress - the organizationAddress to set

    • getUserAdvocateMapping

      public HashMap<Integer,com.compomics.util.experiment.identification.Advocate> getUserAdvocateMapping()
      Returns the user advocates used in this project.
      Returns:
      the user advocates used in this project

    • setUserAdvocateMapping

      public void setUserAdvocateMapping(HashMap<Integer,com.compomics.util.experiment.identification.Advocate> userAdvocateMapping)
      Sets the user advocates used in this project.
      Parameters:
      userAdvocateMapping - the user advocates used in this project

    • getIncludeProteinSequences

      public Boolean getIncludeProteinSequences()
      Returns true if the protein sequences are to be included in the mzid export.
      Returns:
      true if the protein sequences are to be included in the mzid export

    • setIncludeProteinSequences

      public void setIncludeProteinSequences(Boolean includeProteinSequences)
      Set if the protein sequences are to be included in the mzid export.
      Parameters:
      includeProteinSequences - the includeProteinSequences to set