io.repseq.dto

Class VDJCLibraryData

java.lang.Object

io.repseq.dto.VDJCLibraryData

All Implemented Interfaces:

java.lang.Comparable<VDJCLibraryData>

public final class VDJCLibraryData
extends java.lang.Object
implements java.lang.Comparable<VDJCLibraryData>

Constructor Summary

Constructors

Constructor and Description
VDJCLibraryData(long taxonId, java.util.List<java.lang.String> speciesNames, java.util.List<VDJCGeneData> genes, java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> meta, java.util.List<KnownSequenceFragmentData> sequenceFragments)
VDJCLibraryData(VDJCLibraryData other, java.util.List<VDJCGeneData> genes) Creates VDJCLibraryData object from other VDJCLibraryData given new set of genes

Method Summary

Modifier and Type	Method and Description
VDJCLibraryData	addMetaValue(java.lang.String key, java.lang.String value) Add value to the list of values associated with the key.
VDJCLibraryData	clone()
int	compareTo(VDJCLibraryData o)
boolean	equals(java.lang.Object o)
java.util.SortedSet<java.lang.String>	getCitations() Set of citations specified for this library.
java.util.SortedSet<java.lang.String>	getComments() All comment blocks associated with the library
java.util.List<VDJCGeneData>	getGenes()
java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>>	getMeta() Free form meta information for the library, raw meta map
java.lang.String	getMetaValue(java.lang.String key) Returns single value associated with the key from meta section of the library document
java.util.SortedSet<java.lang.String>	getMetaValueSet(java.lang.String key) Returns list of values associated with the key from meta section of the library document
java.util.List<KnownSequenceFragmentData>	getSequenceFragments()
java.util.List<java.lang.String>	getSpeciesNames()
long	getTaxonId()
java.util.SortedSet<java.lang.String>	getWarnings() Warnings, associated with the library.
int	hashCode()
VDJCLibraryData	setMetaValue(java.lang.String key, java.lang.String newValue) Overrides value of field with the specified key.

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VDJCLibraryData

public VDJCLibraryData(VDJCLibraryData other,
                       java.util.List<VDJCGeneData> genes)

Creates VDJCLibraryData object from other VDJCLibraryData given new set of genes

Parameters:

other - VDJCLibraryData to clone properties from

genes - new gene list

VDJCLibraryData

public VDJCLibraryData(long taxonId,
                       java.util.List<java.lang.String> speciesNames,
                       java.util.List<VDJCGeneData> genes,
                       java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> meta,
                       java.util.List<KnownSequenceFragmentData> sequenceFragments)

Method Detail

getTaxonId

public long getTaxonId()

getSpeciesNames

public java.util.List<java.lang.String> getSpeciesNames()

getGenes

public java.util.List<VDJCGeneData> getGenes()

getSequenceFragments

public java.util.List<KnownSequenceFragmentData> getSequenceFragments()

getCitations

public java.util.SortedSet<java.lang.String> getCitations()

Set of citations specified for this library. E.g. can be used to remind academic users to cite specific paper, that this library was published with.

getWarnings

public java.util.SortedSet<java.lang.String> getWarnings()

Warnings, associated with the library. E.g. it is not finished yet (beta release).

getComments

public java.util.SortedSet<java.lang.String> getComments()

All comment blocks associated with the library

getMeta

public java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> getMeta()

Free form meta information for the library, raw meta map

getMetaValueSet

public java.util.SortedSet<java.lang.String> getMetaValueSet(java.lang.String key)

Returns list of values associated with the key from meta section of the library document

Parameters:

key - key

getMetaValue

public java.lang.String getMetaValue(java.lang.String key)

Returns single value associated with the key from meta section of the library document

Parameters:

key - key

setMetaValue

public VDJCLibraryData setMetaValue(java.lang.String key,
                                    java.lang.String newValue)

Overrides value of field with the specified key. All previous values (even if several were associated with the field) will be dropped.

Parameters:

key - key

newValue - new value

addMetaValue

public VDJCLibraryData addMetaValue(java.lang.String key,
                                    java.lang.String value)

Add value to the list of values associated with the key.

Parameters:

key - key

value - value

clone

public VDJCLibraryData clone()

Overrides:

clone in class java.lang.Object

compareTo

public int compareTo(VDJCLibraryData o)

Specified by:

compareTo in interface java.lang.Comparable<VDJCLibraryData>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object