MzidCLIInputBean (PeptideShaker 2.2.2 API)

java.lang.Object
- eu.isas.peptideshaker.cmd.MzidCLIInputBean

```
public class MzidCLIInputBean
extends Object
```
This class is a simple bean wrapping the CLI parameters provided in an Options instance.

Author:

Marc Vaueel, Harald Barsnes

Constructor Summary

Constructors
Constructor and Description

MzidCLIInputBean(org.apache.commons.cli.CommandLine aLine)
Parses a MzidCLI command line and stores the input in the attributes.

Constructors
Constructor and Description
`MzidCLIInputBean(org.apache.commons.cli.CommandLine aLine)` Parses a MzidCLI command line and stores the input in the attributes.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`getContactAddress()` Returns the contact address.
`String`	`getContactEmail()` Returns the contact email.
`String`	`getContactFirstName()` Returns the contact first name.
`String`	`getContactLastName()` Returns the contact last name.
`String`	`getContactUrl()` Returns the contact URL.
`boolean`	`getIncludeProteinSequences()` Returns true if the protein sequences are to be included in the mzid export.
`com.compomics.util.experiment.io.identification.MzIdentMLVersion`	`getMzIdentMLVersion()` Returns the mzIdentML version to use for this file.
`String`	`getOrganizationAddress()` Returns the organization address.
`String`	`getOrganizationMail()` Returns the organization mail.
`String`	`getOrganizationName()` Returns the organization name.
`String`	`getOrganizationUrl()` Returns the organization URL.
`File`	`getOutputFile()` Returns the file where to mzIdentML export will be stored.
`PathSettingsCLIInputBean`	`getPathSettingsCLIInputBean()` Returns the path settings input.
`File`	`getPsdbFile()` Returns the psdb file.
`File`	`getZipFile()` The zip file selected by the user.
`boolean`	`isGzip()` Returns a boolean indicating whether the export should be gzipped.

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

- Constructor Detail
  - MzidCLIInputBean
```
public MzidCLIInputBean(org.apache.commons.cli.CommandLine aLine)
```
    Parses a MzidCLI command line and stores the input in the attributes.
    
    Parameters:
    
    aLine - a MzidCLI command line
- Method Detail
  - getPsdbFile
```
public File getPsdbFile()
```
    Returns the psdb file.
    
    Returns:
    
    the psdb file
  - getZipFile
```
public File getZipFile()
```
    The zip file selected by the user. Null if not set.
    
    Returns:
    
    zip file selected by the user
  - getContactFirstName
```
public String getContactFirstName()
```
    Returns the contact first name.
    
    Returns:
    
    the contact first name
  - getContactLastName
```
public String getContactLastName()
```
    Returns the contact last name.
    
    Returns:
    
    the contact last name
  - getContactEmail
```
public String getContactEmail()
```
    Returns the contact email.
    
    Returns:
    
    the contact email
  - getContactAddress
```
public String getContactAddress()
```
    Returns the contact address.
    
    Returns:
    
    the contact address
  - getContactUrl
```
public String getContactUrl()
```
    Returns the contact URL.
    
    Returns:
    
    the contact URL
  - getOrganizationName
```
public String getOrganizationName()
```
    Returns the organization name.
    
    Returns:
    
    the organization name
  - getOrganizationMail
```
public String getOrganizationMail()
```
    Returns the organization mail.
    
    Returns:
    
    the organization mail
  - getOrganizationAddress
```
public String getOrganizationAddress()
```
    Returns the organization address.
    
    Returns:
    
    the organization address
  - getOrganizationUrl
```
public String getOrganizationUrl()
```
    Returns the organization URL.
    
    Returns:
    
    the organization URL
  - getOutputFile
```
public File getOutputFile()
```
    Returns the file where to mzIdentML export will be stored.
    
    Returns:
    
    the file where to mzIdentML export will be stored
  - 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
  - getMzIdentMLVersion
```
public com.compomics.util.experiment.io.identification.MzIdentMLVersion getMzIdentMLVersion()
```
    Returns the mzIdentML version to use for this file.
    
    Returns:
    
    the mzIdentML version to use for this file
  - getPathSettingsCLIInputBean
```
public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
```
    Returns the path settings input.
    
    Returns:
    
    the path settings input
  - isGzip
```
public boolean isGzip()
```
    Returns a boolean indicating whether the export should be gzipped.
    
    Returns:
    
    a boolean indicating whether the export should be gzipped

Class MzidCLIInputBean

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MzidCLIInputBean

Method Detail

getPsdbFile

getZipFile

getContactFirstName

getContactLastName

getContactEmail

getContactAddress

getContactUrl

getOrganizationName

getOrganizationMail

getOrganizationAddress

getOrganizationUrl

getOutputFile

getIncludeProteinSequences

getMzIdentMLVersion

getPathSettingsCLIInputBean

isGzip