eu.isas.peptideshaker.cmd

Class ReportCLIInputBean

java.lang.Object

eu.isas.peptideshaker.cmd.ReportCLIInputBean

public class ReportCLIInputBean
extends Object

This class is a simple bean wrapping the CLI parameters provided in an Options instance.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
ReportCLIInputBean(org.apache.commons.cli.CommandLine aLine) Construct a FollowUpCLIInputBean from an Apache CLI instance.

Method Summary

Modifier and Type	Method and Description
boolean	documentationExportNeeded() Indicates whether a documentation export is required by the user.
boolean	exportNeeded() Indicates whether a report export is needed.
ArrayList<String>	getDocumentationTypes() Returns the type of documentation required by the user.
PathSettingsCLIInputBean	getPathSettingsCLIInputBean() Returns the path settings provided by the user.
File	getPsdbFile() Returns the psdb file from which the information can be obtained.
String	getReportNamePrefix() Returns the report name prefix.
File	getReportOutputFolder() Returns the report output folder.
ArrayList<String>	getReportTypes() Returns the types of output required by the user.
File	getZipFile() The zip file selected by the user.
boolean	isGzip() Returns a boolean indicating whether the export should be gzipped.
boolean	reportExportNeeded() Indicates whether a report export is required by the user.
void	setReportNamePrefix(String reportNamePrefix) Set the report name prefix.
void	setReportOutputFolder(File outputFolder) Set the report output folder.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReportCLIInputBean

public ReportCLIInputBean(org.apache.commons.cli.CommandLine aLine)

Construct a FollowUpCLIInputBean from an Apache CLI instance.

Parameters:

aLine - the command line

Method Detail

getPsdbFile

public File getPsdbFile()

Returns the psdb file from which the information can be obtained.

Returns:

the psdb file from which the information can be obtained

getZipFile

public File getZipFile()

The zip file selected by the user. Null if not set.

Returns:

zip file selected by the user

getReportOutputFolder

public File getReportOutputFolder()

Returns the report output folder.

Returns:

the output folder

setReportOutputFolder

public void setReportOutputFolder(File outputFolder)

Set the report output folder.

Parameters:

outputFolder - the report output folder

getReportNamePrefix

public String getReportNamePrefix()

Returns the report name prefix.

Returns:

the report name prefix

setReportNamePrefix

public void setReportNamePrefix(String reportNamePrefix)

Set the report name prefix.

Parameters:

reportNamePrefix - the report output folder

getReportTypes

public ArrayList<String> getReportTypes()

Returns the types of output required by the user.

Returns:

the types of output

getDocumentationTypes

public ArrayList<String> getDocumentationTypes()

Returns the type of documentation required by the user.

Returns:

the type of documentation types

exportNeeded

public boolean exportNeeded()

Indicates whether a report export is needed.

Returns:

true if a report export is needed

reportExportNeeded

public boolean reportExportNeeded()

Indicates whether a report export is required by the user.

Returns:

true if a report export is required

documentationExportNeeded

public boolean documentationExportNeeded()

Indicates whether a documentation export is required by the user.

Returns:

true if documentation export is require

getPathSettingsCLIInputBean

public PathSettingsCLIInputBean getPathSettingsCLIInputBean()

Returns the path settings provided by the user.

Returns:

the path settings provided by the user

isGzip

public boolean isGzip()

Returns a boolean indicating whether the export should be gzipped.

Returns:

a boolean indicating whether the export should be gzipped