com.compomics.util.io.export

Class ExportScheme

java.lang.Object

com.compomics.util.io.export.ExportScheme

All Implemented Interfaces:

Serializable

public class ExportScheme
extends Object
implements Serializable

This class allows creating a standard output scheme.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ExportScheme(String name, boolean editable, ArrayList<String> sectionList, HashMap<String,ArrayList<ExportFeature>> exportFeatures, String separator, boolean indexes, boolean header, int separationLines, boolean includeSectionTitles, boolean validatedOnly, boolean includeDecoys) Constructor.
ExportScheme(String name, boolean editable, HashMap<String,ArrayList<ExportFeature>> exportFeatures, String separator, boolean indexes, boolean header, int separationLines, boolean includeSectionTitles, boolean validatedOnly, boolean includeDecoys) Constructor.
ExportScheme(String name, boolean editable, HashMap<String,ArrayList<ExportFeature>> exportFeatures, String separator, boolean indexes, boolean header, int separationLines, boolean includeSectionTitles, boolean validatedOnly, boolean includeDecoys, String mainTitle) Constructor.

Method Summary

Modifier and Type	Method and Description
void	addExportFeature(String section, ExportFeature exportFeature) Adds an export feature to the desired section.
ArrayList<ExportFeature>	getExportFeatures(String section) Returns the export features to be included in the given section.
String	getMainTitle() Returns the main title of the report.
String	getName() Returns the name of the scheme.
ArrayList<String>	getSections() returns the list of sections to be included in the scheme.
int	getSeparationLines() Returns the number of lines to be used to separate the sections.
String	getSeparator() Returns the column separator.
boolean	isEditable() Indicates whether the scheme is editable.
boolean	isHeader() Indicates whether column header shall be used.
Boolean	isIncludeDecoy() Indicates whether decoy hits should be included.
boolean	isIncludeSectionTitles() Indicates whether section titles shall be used.
boolean	isIndexes() Indicates whether lines shall be indexed.
Boolean	isValidatedOnly() Indicates whether only validated results should be exported.
void	removeSection(String sectionName) Removes an entire section from the mapping.
void	setEditable(boolean editable) Sets whether the scheme is editable.
void	setExportFeatures(String section, ArrayList<ExportFeature> exportFeatures) Sets the export features of a given section.
void	setIncludeDecoy(Boolean includeDecoy) Sets whether decoy hits should be included.
void	setName(String name) Sets the name of the scheme.
void	setValidatedOnly(Boolean validatedOnly) Sets whether only validated results should be exported.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExportScheme

public ExportScheme(String name,
                    boolean editable,
                    HashMap<String,ArrayList<ExportFeature>> exportFeatures,
                    String separator,
                    boolean indexes,
                    boolean header,
                    int separationLines,
                    boolean includeSectionTitles,
                    boolean validatedOnly,
                    boolean includeDecoys,
                    String mainTitle)

Constructor. Here sections will appear in a random order.

Parameters:

name - the name of the scheme

editable - a boolean indicating whether the scheme can be edited by the user

exportFeatures - list of features to be included in the report

separator - the column separator to be used

indexes - indicates whether lines shall be indexed

header - indicates whether column headers shall be included

separationLines - the number of lines to use for section separation

includeSectionTitles - indicates whether section titles shall be used

mainTitle - the title of the report

validatedOnly - Indicates whether only validated matches should be included

includeDecoys - Indicates whether decoy matches should be included

ExportScheme

public ExportScheme(String name,
                    boolean editable,
                    ArrayList<String> sectionList,
                    HashMap<String,ArrayList<ExportFeature>> exportFeatures,
                    String separator,
                    boolean indexes,
                    boolean header,
                    int separationLines,
                    boolean includeSectionTitles,
                    boolean validatedOnly,
                    boolean includeDecoys)

Constructor. This report will not contain any title.

Parameters:

name - the name of the scheme

editable - a boolean indicating whether the scheme can be edited by the user

sectionList - ordered list of the sections included in the report

exportFeatures - list of features to be included in the report

separator - the column separator to be used

indexes - indicates whether lines shall be indexed

header - indicates whether column headers shall be included

separationLines - the number of lines to use for section separation

includeSectionTitles - indicates whether section titles shall be used

validatedOnly - Indicates whether only validated matches should be included

includeDecoys - Indicates whether decoy matches should be included

ExportScheme

public ExportScheme(String name,
                    boolean editable,
                    HashMap<String,ArrayList<ExportFeature>> exportFeatures,
                    String separator,
                    boolean indexes,
                    boolean header,
                    int separationLines,
                    boolean includeSectionTitles,
                    boolean validatedOnly,
                    boolean includeDecoys)

Constructor. This report will not contain any title and sections will appear in a random order.

Parameters:

name - the name of the scheme

editable - a boolean indicating whether the scheme can be edited by the user

exportFeatures - list of features to be included in the report

separator - the column separator to be used

indexes - indicates whether lines shall be indexed

header - indicates whether column headers shall be included

separationLines - the number of lines to use for section separation

includeSectionTitles - indicates whether section titles shall be used

validatedOnly - Indicates whether only validated matches should be included

includeDecoys - Indicates whether decoy matches should be included

Method Detail

getSeparator

public String getSeparator()

Returns the column separator.

Returns:

the column separator

isIndexes

public boolean isIndexes()

Indicates whether lines shall be indexed.

Returns:

a boolean indicating whether lines shall be indexed

isHeader

public boolean isHeader()

Indicates whether column header shall be used.

Returns:

a boolean indicating whether column header shall be used

getSeparationLines

public int getSeparationLines()

Returns the number of lines to be used to separate the sections.

Returns:

the number of lines to be used to separate the sections

isIncludeSectionTitles

public boolean isIncludeSectionTitles()

Indicates whether section titles shall be used.

Returns:

a boolean indicating whether section titles shall be used

getSections

public ArrayList<String> getSections()

returns the list of sections to be included in the scheme.

Returns:

the list of sections to be included in the scheme

getExportFeatures

public ArrayList<ExportFeature> getExportFeatures(String section)

Returns the export features to be included in the given section.

Parameters:

section - the section of interest

Returns:

the list of export features to export in this section

setExportFeatures

public void setExportFeatures(String section,
                              ArrayList<ExportFeature> exportFeatures)

Sets the export features of a given section. If a section already exists it will be silently overwritten.

Parameters:

section - the name of the section

exportFeatures - the export features to include in that section

addExportFeature

public void addExportFeature(String section,
                             ExportFeature exportFeature)

Adds an export feature to the desired section. If the section does not exist it will be created.

Parameters:

section - the name of the section

exportFeature - the export feature to add

removeSection

public void removeSection(String sectionName)

Removes an entire section from the mapping.

Parameters:

sectionName - the section name

getMainTitle

public String getMainTitle()

Returns the main title of the report. Null if none.

Returns:

the main title of the report.

getName

public String getName()

Returns the name of the scheme.

Returns:

the name of the scheme

setName

public void setName(String name)

Sets the name of the scheme.

Parameters:

name - the name of the scheme

isEditable

public boolean isEditable()

Indicates whether the scheme is editable.

Returns:

a boolean indicating whether the scheme is editable

setEditable

public void setEditable(boolean editable)

Sets whether the scheme is editable.

Parameters:

editable - a boolean indicating whether the scheme shall be editable

isValidatedOnly

public Boolean isValidatedOnly()

Indicates whether only validated results should be exported.

Returns:

whether only validated results should be exported

setValidatedOnly

public void setValidatedOnly(Boolean validatedOnly)

Sets whether only validated results should be exported.

Parameters:

validatedOnly - whether only validated results should be exported

isIncludeDecoy

public Boolean isIncludeDecoy()

Indicates whether decoy hits should be included.

Returns:

whether decoy hits should be included

setIncludeDecoy

public void setIncludeDecoy(Boolean includeDecoy)

Sets whether decoy hits should be included.

Parameters:

includeDecoy - whether decoy hits should be included