ProjectDetails (PeptideShaker 2.2.2 API)

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:

Serialized Form

Field Summary
- Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject
  NO_KEY

Constructor Summary

Constructors
Constructor and Description

ProjectDetails()
Constructor.

Constructors
Constructor and Description
`ProjectDetails()` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addIdentificationFiles(File identificationFile)` Adds an identification file to the list of loaded identification files.
`void`	`addSpectrumFilePath(String spectrumFilePath)` Attaches a spectrum file to the project.
`HashMap<String,ArrayList<String>>`	`getAlgorithmNameToVersionsMap()` Returns the different identification algorithm versions used in a map: algorithm name > versions.
`String`	`getContactAddress()` Returns the address of the contact for the mzIdentML dataset.
`String`	`getContactEmail()` Returns the e-mail of the contact for the mzIdentML dataset.
`String`	`getContactFirstName()` Returns the first name of the contact for the mzIdentML dataset.
`String`	`getContactLastName()` Returns the last name of the contact for the mzIdentML dataset.
`String`	`getContactUrl()` Returns the URL of the contact for the mzIdentML dataset.
`Date`	`getCreationDate()` Getter for the creation date of the project.
`String`	`getFastaFile()` Returns the path to the FASTA file.
`ArrayList<Integer>`	`getIdentificationAlgorithms()` Returns a list of identification algorithms used based on the identification files of the project.
`HashMap<String,ArrayList<String>>`	`getIdentificationAlgorithmsForFile(String idFileName)` Returns the identification algorithms used to create the id file in map: algorithm name > algorithm version.
`ArrayList<String>`	`getIdentificationFiles()` Getter for all identification files loaded.
`Boolean`	`getIncludeProteinSequences()` Returns true if the protein sequences are to be included in the mzid export.
`String`	`getMzIdentMLOutputFile()` Returns the mzIdentML output file.
`String`	`getOrganizationAddress()` Returns the address of the organization for the mzIdentML dataset.
`String`	`getOrganizationEmail()` Returns the e-mail of the organization for the mzIdentML dataset.
`String`	`getOrganizationName()` Returns the name of the organization for the mzIdentML dataset.
`String`	`getOrganizationUrl()` Returns the URL of the organization for the mzIdentML dataset.
`String`	`getPeptideShakerVersion()` Returns the PeptideShaker version used to create the project.
`com.compomics.util.pride.prideobjects.ContactGroup`	`getPrideContactGroup()` Returns the PRIDE contact group.
`String`	`getPrideExperimentDescription()` Returns the PRIDE experiment project description.
`String`	`getPrideExperimentLabel()` Returns the PRIDE experiment label.
`String`	`getPrideExperimentProjectTitle()` Returns the PRIDE experiment project title.
`String`	`getPrideExperimentTitle()` Returns the PRIDE experiment title.
`com.compomics.util.pride.prideobjects.Instrument`	`getPrideInstrument()` Returns the PRIDE instrument.
`String`	`getPrideOutputFolder()` Returns the PRIDE output folder.
`com.compomics.util.pride.prideobjects.Protocol`	`getPrideProtocol()` Returns the PRIDE protocol.
`com.compomics.util.pride.prideobjects.ReferenceGroup`	`getPrideReferenceGroup()` Returns the PRIDE reference group.
`com.compomics.util.pride.prideobjects.Sample`	`getPrideSample()` Returns the PRIDE sample.
`String`	`getReport()` Returns the report created during the loading of the project.
`Set<String>`	`getSpectrumFileNames()` Returns the name of the input spectrum files as a set.
`String`	`getSpectrumFilePath(String fileName)` Returns the path to the file corresponding to the given name.
`HashMap<Integer,com.compomics.util.experiment.identification.Advocate>`	`getUserAdvocateMapping()` Returns the user advocates used in this project.
`boolean`	`hasIdentificationAlgorithms()` Returns true if the identification algorithms are stored.
`void`	`setContactAddress(String contactAddress)` SEt the address of the contact for the mzIdentML dataset.
`void`	`setContactEmail(String contactEmail)` Set the e-mail of the contact for the mzIdentML dataset.
`void`	`setContactFirstName(String contactFirstName)` Set the first name of the contact for the mzIdentML dataset.
`void`	`setContactLastName(String contactLastName)` Set the last name of the contact for the mzIdentML dataset.
`void`	`setContactUrl(String contactUrl)` Set the first URL of the contact for the mzIdentML dataset.
`void`	`setCreationDate(Date creationDate)` Setter the creation date of the project.
`void`	`setFastaFile(File fastaFile)` Set the path to the FASTA file.
`void`	`setIdentificationAlgorithmsForFile(String idFileName, HashMap<String,ArrayList<String>> fileIdentificationAlgorithms)` Sets the identification algorithms used to create an identification file.
`void`	`setIncludeProteinSequences(Boolean includeProteinSequences)` Set if the protein sequences are to be included in the mzid export.
`void`	`setMzIdentOutputFile(String mzIdentMLOutputFile)` Set the mzIdentML output file.
`void`	`setOrganizationAddress(String organizationAddress)` Set the address of the organization for the mzIdentML dataset.
`void`	`setOrganizationEmail(String organizationEmail)` Set the name of the organization for the mzIdentML dataset.
`void`	`setOrganizationName(String organizationName)` Set the name of the organization for the mzIdentML dataset.
`void`	`setOrganizationUrl(String organizationUrl)` Set the URL of the organization for the mzIdentML dataset.
`void`	`setPeptideShakerVersion(String peptideShakerVersion)` Sets the PeptideShaker version used to create the project.
`void`	`setPrideContactGroup(com.compomics.util.pride.prideobjects.ContactGroup prideContactGroup)` Set the PRIDE contact group.
`void`	`setPrideExperimentDescription(String prideExperimentDescription)` Set the PRIDE experiment project description.
`void`	`setPrideExperimentLabel(String prideExperimentLabel)` Sets the PRIDE experiment label.
`void`	`setPrideExperimentProjectTitle(String prideExperimentProjectTitle)` Set the PRIDE experiment project title.
`void`	`setPrideExperimentTitle(String prideExperimentTitle)` Sets the PRIDE experiment title.
`void`	`setPrideInstrument(com.compomics.util.pride.prideobjects.Instrument prideInstrument)` Set the the PRIDE instrument.
`void`	`setPrideOutputFolder(String prideOutputFolder)` Set the PRIDE output folder.
`void`	`setPrideProtocol(com.compomics.util.pride.prideobjects.Protocol prideProtocol)` Set the PRIDE protocol.
`void`	`setPrideReferenceGroup(com.compomics.util.pride.prideobjects.ReferenceGroup prideReferenceGroup)` Set the PRIDE reference group.
`void`	`setPrideSample(com.compomics.util.pride.prideobjects.Sample prideSample)` Set the PRIDE sample.
`void`	`setReport(String report)` Set the report created during the loading of the project.
`void`	`setUserAdvocateMapping(HashMap<Integer,com.compomics.util.experiment.identification.Advocate> userAdvocateMapping)` Sets the user advocates used in this project.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ProjectDetails
```
public ProjectDetails()
```
    Constructor.
- Method Detail
  - 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

Class ProjectDetails

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

Constructor Summary

Method Summary

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

Methods inherited from class java.lang.Object

Constructor Detail

ProjectDetails

Method Detail

getIdentificationFiles

addIdentificationFiles

addSpectrumFilePath

getSpectrumFileNames

getSpectrumFilePath

setFastaFile

getFastaFile

getCreationDate

setCreationDate

getPeptideShakerVersion

setPeptideShakerVersion

getReport

setReport

getPrideExperimentTitle

setPrideExperimentTitle

getPrideExperimentLabel

setPrideExperimentLabel

getPrideExperimentProjectTitle

setPrideExperimentProjectTitle

getPrideExperimentDescription

setPrideExperimentDescription

getPrideReferenceGroup

setPrideReferenceGroup

getPrideContactGroup

setPrideContactGroup

getPrideSample

setPrideSample

getPrideProtocol

setPrideProtocol

getPrideInstrument

setPrideInstrument

getPrideOutputFolder

setPrideOutputFolder

getMzIdentMLOutputFile

setMzIdentOutputFile

hasIdentificationAlgorithms

getIdentificationAlgorithms

getAlgorithmNameToVersionsMap

getIdentificationAlgorithmsForFile

setIdentificationAlgorithmsForFile

getContactFirstName

setContactFirstName

getContactLastName

setContactLastName

getContactEmail

setContactEmail

getContactUrl

setContactUrl

getContactAddress

setContactAddress

getOrganizationName

setOrganizationName

getOrganizationEmail

setOrganizationEmail

getOrganizationUrl

setOrganizationUrl

getOrganizationAddress

setOrganizationAddress

getUserAdvocateMapping

setUserAdvocateMapping

getIncludeProteinSequences

setIncludeProteinSequences