de.mpg.biochem.mars.molecule

Class AbstractMarsRecord

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMarsRecord

All Implemented Interfaces:

JsonConvertibleRecord, MarsRecord

Direct Known Subclasses:

AbstractMarsMetadata, AbstractMolecule, OLDMarsMetadata

public abstract class AbstractMarsRecord
extends AbstractJsonConvertibleRecord
implements MarsRecord

Abstract superclass for all MarsRecord types: Molecule and MarsMetadata. All MarsRecords have a basic set of properties including a UID, notes, tags, parameters, a MarsTable, MarsRegions, and MarsPositions. MarsRecords can be serialized to and from Json.

This basic set of properties is extended for storage of molecule information and metadata information in Molecule, AbstractMolecule, MarsMetadata, AbstractMarsMetadata.

Field Summary

Fields

Modifier and Type	Field and Description
protected MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>>	parent Reference to MoleculeArchive containing the record.

Constructor Summary

Constructors

Constructor and Description
AbstractMarsRecord() Constructor for creating an empty MarsRecord.
AbstractMarsRecord(java.lang.String UID) Constructor for creating an empty MarsRecord with the specified UID.

Method Summary

Modifier and Type	Method and Description
void	addNote(java.lang.String note) Add to any notes already in the record.
void	addTag(java.lang.String tag) Add a string tag to the record.
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
boolean	getBooleanParameter(java.lang.String parameter) Get the value of a boolean parameter.
java.lang.String	getNotes() Get notes for this record.
double	getParameter(java.lang.String parameter) Get the value of a parameter.
java.util.LinkedHashMap<java.lang.String,java.lang.Object>	getParameters() Get the map for all parameters.
MarsPosition	getPosition(java.lang.String name) Get a MarsPosition.
java.util.Set<java.lang.String>	getPositionNames() Get the set of position names contained in this record.
java.util.LinkedHashMap<java.lang.String,MarsPosition>	getPositions() Get the map for all positions.
MarsRegion	getRegion(java.lang.String name) Get a MarsRegion.
java.util.Set<java.lang.String>	getRegionNames() Get the set of region names contained in this record.
java.util.LinkedHashMap<java.lang.String,MarsRegion>	getRegions() Get the map for all regions.
java.lang.String	getStringParameter(java.lang.String parameter) Get the value of a string parameter.
java.util.LinkedHashSet<java.lang.String>	getTags() Get the set of all tags.
java.lang.String[]	getTagsArray() Get an array list of all tags.
java.lang.String	getUID() Get the UID for this record.
boolean	hasBooleanParameter(java.lang.String parameter) Returns true if the boolean parameter exists.
boolean	hasDoubleParameter(java.lang.String parameter) Returns true if the double parameter exists.
boolean	hasNoTags() Check if the record has no tags.
boolean	hasParameter(java.lang.String parameter) Returns true if any type of parameters has the name give.
boolean	hasPosition(java.lang.String name) Check if the record contains a MarsPosition using the name.
boolean	hasRegion(java.lang.String name) Check if the record contains a MarsRegion using the name.
boolean	hasStringParameter(java.lang.String parameter) Returns true if the string parameter exists.
boolean	hasTag(java.lang.String tag) Check if the record has a tag.
void	merge(MarsRecord record) Merge another MarsRecord into this one.
void	putPosition(MarsPosition positionOfInterest) Add or update a MarsPosition.
void	putRegion(MarsRegion regionOfInterest) Add or update a MarsRegion.
void	removeAllParameters() Remove all parameter values from the record.
void	removeAllPositions() Remove all positions from the record.
void	removeAllRegions() Remove all regions from the record.
void	removeAllTags() Remove all tags from the record.
void	removeParameter(java.lang.String parameter) Remove parameter.
void	removePosition(java.lang.String name) Remove a MarsPosition from the record using the name.
void	removeRegion(java.lang.String name) Remove a MarsRegion from the record using the name.
void	removeTag(java.lang.String tag) Remove a string tag from the record.
void	setNotes(java.lang.String notes) Sets the notes for this record.
void	setParameter(java.lang.String parameter, boolean value) Add or update a parameter value.
void	setParameter(java.lang.String parameter, double value) Add or update a parameter value.
void	setParameter(java.lang.String parameter, java.lang.String value) Add or update a parameter value.
void	setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive) Set the parent MoleculeArchive that this record is stored in.

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Field Detail

parent

protected MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> parent

Reference to MoleculeArchive containing the record.

Constructor Detail

AbstractMarsRecord

public AbstractMarsRecord()

Constructor for creating an empty MarsRecord.

AbstractMarsRecord

public AbstractMarsRecord(java.lang.String UID)

Constructor for creating an empty MarsRecord with the specified UID.

Parameters:

UID - The unique identifier for this MarsRecord.

Method Detail

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Specified by:

createIOMaps in class AbstractJsonConvertibleRecord

getUID

public java.lang.String getUID()

Get the UID for this record.

Specified by:

getUID in interface MarsRecord

Returns:

Returns the UID.

getNotes

public java.lang.String getNotes()

Get notes for this record. Notes can be added during manual sorting to point out a feature or important detail about the current record.

Specified by:

getNotes in interface MarsRecord

Returns:

Returns a string containing any notes associated with this record.

setNotes

public void setNotes(java.lang.String notes)

Sets the notes for this record. Notes can be added during manual sorting to point out a feature or important detail about the current record.

Specified by:

setNotes in interface MarsRecord

Parameters:

notes - Any notes about this molecule.

addNote

public void addNote(java.lang.String note)

Add to any notes already in the record.

Specified by:

addNote in interface MarsRecord

Parameters:

note - String with the note to add to the record.

addTag

public void addTag(java.lang.String tag)

Add a string tag to the record. Tags are used for marking individual record to sorting and processing with subsets of molecules.

Specified by:

addTag in interface MarsRecord

Parameters:

tag - The string tag to be added.

hasTag

public boolean hasTag(java.lang.String tag)

Check if the record has a tag.

Specified by:

hasTag in interface MarsRecord

Parameters:

tag - The string tag to check for.

Returns:

Returns true if the record has the tag and false if not.

hasNoTags

public boolean hasNoTags()

Check if the record has no tags.

Specified by:

hasNoTags in interface MarsRecord

Returns:

Returns true if the record has no tags.

getTags

public java.util.LinkedHashSet<java.lang.String> getTags()

Get the set of all tags.

Specified by:

getTags in interface MarsRecord

Returns:

Returns the set of tags for this record.

getTagsArray

public java.lang.String[] getTagsArray()

Get an array list of all tags.

Specified by:

getTagsArray in interface MarsRecord

Returns:

Returns the set of tags for this record as an array.

removeTag

public void removeTag(java.lang.String tag)

Remove a string tag from the record.

Specified by:

removeTag in interface MarsRecord

Parameters:

tag - The string tag to remove.

removeAllTags

public void removeAllTags()

Remove all tags from the record.

Specified by:

removeAllTags in interface MarsRecord

setParameter

public void setParameter(java.lang.String parameter,
                         double value)

Add or update a parameter value. Parameters are used to store single values associated with the record.

Specified by:

setParameter in interface MarsRecord

Parameters:

parameter - The string parameter name.

value - The double value to set for the parameter name.

setParameter

public void setParameter(java.lang.String parameter,
                         java.lang.String value)

Add or update a parameter value.

Specified by:

setParameter in interface MarsRecord

Parameters:

parameter - The string parameter name.

value - The string value to set for the parameter name.

setParameter

public void setParameter(java.lang.String parameter,
                         boolean value)

Add or update a parameter value.

Specified by:

setParameter in interface MarsRecord

Parameters:

parameter - The string parameter name.

value - The boolean value to set for the parameter name.

removeAllParameters

public void removeAllParameters()

Remove all parameter values from the record.

Specified by:

removeAllParameters in interface MarsRecord

removeParameter

public void removeParameter(java.lang.String parameter)

Remove parameter. Removes the name and value pair.

Specified by:

removeParameter in interface MarsRecord

Parameters:

parameter - The parameter name to remove.

getParameter

public double getParameter(java.lang.String parameter)

Get the value of a parameter.

Specified by:

getParameter in interface MarsRecord

Parameters:

parameter - The string parameter name to retrieve the value for.

Returns:

Returns the double value for the parameter name given.

getStringParameter

public java.lang.String getStringParameter(java.lang.String parameter)

Get the value of a string parameter.

Specified by:

getStringParameter in interface MarsRecord

Parameters:

parameter - The string parameter name to retrieve the value for.

Returns:

Returns the string value for the parameter name given.

getBooleanParameter

public boolean getBooleanParameter(java.lang.String parameter)

Get the value of a boolean parameter.

Specified by:

getBooleanParameter in interface MarsRecord

Parameters:

parameter - The parameter name to retrieve.

Returns:

Returns the boolean value for the parameter name given.

hasParameter

public boolean hasParameter(java.lang.String parameter)

Returns true if any type of parameters has the name give.

Specified by:

hasParameter in interface MarsRecord

Parameters:

parameter - The parameter name to check for.

Returns:

Returns true if a parameter with the name exists.

hasDoubleParameter

public boolean hasDoubleParameter(java.lang.String parameter)

Returns true if the double parameter exists.

Specified by:

hasDoubleParameter in interface MarsRecord

Parameters:

parameter - The double parameter name to check for.

Returns:

Returns true if a parameter with this name exists.

hasStringParameter

public boolean hasStringParameter(java.lang.String parameter)

Returns true if the string parameter exists.

Specified by:

hasStringParameter in interface MarsRecord

Parameters:

parameter - The string parameter name to check for.

Returns:

Returns true if a parameter with this name exists.

hasBooleanParameter

public boolean hasBooleanParameter(java.lang.String parameter)

Returns true if the boolean parameter exists.

Specified by:

hasBooleanParameter in interface MarsRecord

Parameters:

parameter - The boolean parameter name to check for.

Returns:

Returns true if a parameter with this name exists.

getParameters

public java.util.LinkedHashMap<java.lang.String,java.lang.Object> getParameters()

Get the map for all parameters.

Specified by:

getParameters in interface MarsRecord

Returns:

Returns the map of parameter names to values.

putRegion

public void putRegion(MarsRegion regionOfInterest)

Add or update a MarsRegion. This can be a region of interest for further analysis steps: slope calculations or KCP calculations KCPCommand. Region names are unique. If a region that has this name already exists in the record it will be overwritten by this method.

Specified by:

putRegion in interface MarsRecord

Parameters:

regionOfInterest - The region to add to the record.

getRegion

public MarsRegion getRegion(java.lang.String name)

Get a MarsRegion. Region names are unique. Only one copy of each region can be stored in the record.

Specified by:

getRegion in interface MarsRecord

Parameters:

name - The name of the region to retrieve.

Returns:

The MarsRegion with the name given.

hasRegion

public boolean hasRegion(java.lang.String name)

Check if the record contains a MarsRegion using the name.

Specified by:

hasRegion in interface MarsRecord

Parameters:

name - The name of the region to check for.

Returns:

True if a region with name exists, false otherwise.

removeRegion

public void removeRegion(java.lang.String name)

Remove a MarsRegion from the record using the name.

Specified by:

removeRegion in interface MarsRecord

Parameters:

name - The name of the region to remove.

removeAllRegions

public void removeAllRegions()

Remove all regions from the record.

Specified by:

removeAllRegions in interface MarsRecord

getRegionNames

public java.util.Set<java.lang.String> getRegionNames()

Get the set of region names contained in this record.

Specified by:

getRegionNames in interface MarsRecord

Returns:

The set of region names.

getRegions

public java.util.LinkedHashMap<java.lang.String,MarsRegion> getRegions()

Get the map for all regions.

Specified by:

getRegions in interface MarsRecord

Returns:

The map containing all regions.

putPosition

public void putPosition(MarsPosition positionOfInterest)

Add or update a MarsPosition. This can be a position of interest for further analysis steps. Position names are unique. If a position with has this name already exists in the record it will be overwritten by this method.

Specified by:

putPosition in interface MarsRecord

Parameters:

positionOfInterest - The position to add to the record.

getPosition

public MarsPosition getPosition(java.lang.String name)

Get a MarsPosition. Position names are unique. Only one copy of each region can be stored in the record.

Specified by:

getPosition in interface MarsRecord

Parameters:

name - The name of the position to retrieve.

Returns:

The MarsPosition with the name given.

hasPosition

public boolean hasPosition(java.lang.String name)

Check if the record contains a MarsPosition using the name.

Specified by:

hasPosition in interface MarsRecord

Parameters:

name - The name of the position to check for.

Returns:

True if the position exists, false otherwise.

removePosition

public void removePosition(java.lang.String name)

Remove a MarsPosition from the record using the name.

Specified by:

removePosition in interface MarsRecord

Parameters:

name - The name of the position to remove.

removeAllPositions

public void removeAllPositions()

Remove all positions from the record.

Specified by:

removeAllPositions in interface MarsRecord

getPositionNames

public java.util.Set<java.lang.String> getPositionNames()

Get the set of position names contained in this record.

Specified by:

getPositionNames in interface MarsRecord

Returns:

The set of MarsPosition names.

getPositions

public java.util.LinkedHashMap<java.lang.String,MarsPosition> getPositions()

Get the map for all positions.

Specified by:

getPositions in interface MarsRecord

Returns:

The map containing all positions.

merge

public void merge(MarsRecord record)

Merge another MarsRecord into this one.

Specified by:

merge in interface MarsRecord

Parameters:

record - The record to merge.

setParent

public void setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive)

Set the parent MoleculeArchive that this record is stored in.

Specified by:

setParent in interface MarsRecord

Parameters:

archive - The MoleculeArchive holding this record.