Sample (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.security.PermissionsAware
- - net.sourceforge.seqware.common.model.Sample

All Implemented Interfaces:: Serializable, Comparable<Sample>, Annotatable<SampleAttribute>, FirstTierModel, ParentAccessionModel

public class Sample
extends PermissionsAware
implements Serializable, Comparable<Sample>, ParentAccessionModel, Annotatable<SampleAttribute>, FirstTierModel

See Also:: Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

static String GEO_REACTION_ID_ATTR_TAG
The presence of this attribute is used to identify that the sample is a library

Fields
Modifier and Type	Field and Description
`static String`	`GEO_REACTION_ID_ATTR_TAG` The presence of this attribute is used to identify that the sample is a library

Constructor Summary

Constructors
Constructor and Description

Sample()
Constructor for Sample.

Constructors
Constructor and Description
`Sample()` Constructor for Sample.

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(Sample that)`
`boolean`	`equals(Object other)`
`String`	`getAdapters()` Getter for the field `adapters`.
`String`	`getAlias()` Getter for the field `alias`.
`Set<SampleAttribute>`	`getAnnotations()` Get the annotations for this model
`String`	`getAnonymizedName()` Getter for the field `anonymizedName`.
`Set<Sample>`	`getChildren()` Getter for the field `children`.
`Integer`	`getCountFile()` Getter for the field `countFile`.
`Date`	`getCreateTimestamp()` Getter for the field `createTimestamp`.
`String`	`getDescription()` Getter for the field `description`.
`Integer`	`getExpectedNumReads()` Getter for the field `expectedNumReads`.
`Integer`	`getExpectedNumRuns()` Getter for the field `expectedNumRuns`.
`Integer`	`getExpectedNumSpots()` Getter for the field `expectedNumSpots`.
`Experiment`	`getExperiment()` Getter for the field `experiment`.
`String`	`getIndividualName()` Getter for the field `individualName`.
`Boolean`	`getIsHasFile()` Getter for the field `isHasFile`.
`Boolean`	`getIsSelected()` Getter for the field `isSelected`.
`SortedSet<IUS>`	`getIUS()` getIUS.
`String`	`getJsonEscapeDescription()` getJsonEscapeDescription.
`String`	`getJsonEscapeName()` getJsonEscapeName.
`String`	`getJsonEscapeTitle()` getJsonEscapeTitle.
`SortedSet<Lane>`	`getLanes()` Getter for the field `lanes`.
`String`	`getName()` Getter for the field `name`.
`Organism`	`getOrganism()` Getter for the field `organism`.
`Integer`	`getOrganismId()` Getter for the field `organismId`.
`Registration`	`getOwner()` Getter for the field `owner`.
`Set<Sample>`	`getParents()` Getter for the field `parents`.
`Set<Processing>`	`getProcessings()` Getter for the field `processings`.
`String`	`getRegions()` Getter for the field `regions`.
`Set<SampleAttribute>`	`getSampleAttributes()` Getter for the field `sampleAttributes`.
`Integer`	`getSampleId()` Getter for the field `sampleId`.
`static long`	`getSerialVersionUID()` Getter for the field `serialVersionUID`.
`Boolean`	`getSkip()` Getter for the field `skip`.
`String`	`getStrExpectedNumReads()` Getter for the field `strExpectedNumReads`.
`String`	`getStrExpectedNumRuns()` Getter for the field `strExpectedNumRuns`.
`Integer`	`getSwAccession()` Getter for the field `swAccession`.
`String`	`getTags()` Getter for the field `tags`.
`String`	`getTitle()` Getter for the field `title`.
`String`	`getType()` Getter for the field `type`.
`Date`	`getUpdateTimestamp()` Getter for the field `updateTimestamp`.
`boolean`	`givesPermissionInternal(Registration registration, Set<Integer> considered)` Short-circuit permission checking by providing a set of entities that have already been checked
`int`	`hashCode()`
`void`	`setAdapters(String adapters)` Setter for the field `adapters`.
`void`	`setAlias(String alias)` Setter for the field `alias`.
`void`	`setAnonymizedName(String anonymizedName)` Setter for the field `anonymizedName`.
`void`	`setChildren(Set<Sample> children)` Setter for the field `children`.
`void`	`setCountFile(Integer countFile)` Setter for the field `countFile`.
`void`	`setCreateTimestamp(Date createTimestamp)` Setter for the field `createTimestamp`.
`void`	`setDescription(String description)` Setter for the field `description`.
`void`	`setExpectedNumReads(Integer expectedNumReads)` Setter for the field `expectedNumReads`.
`void`	`setExpectedNumRuns(Integer expectedNumRuns)` Setter for the field `expectedNumRuns`.
`void`	`setExpectedNumSpots(Integer expectedNumSpots)` Setter for the field `expectedNumSpots`.
`void`	`setExperiment(Experiment experiment)` Setter for the field `experiment`.
`void`	`setIndividualName(String individualName)` Setter for the field `individualName`.
`void`	`setIsHasFile(Boolean isHasFile)` Setter for the field `isHasFile`.
`void`	`setIsSelected(Boolean isSelected)` Setter for the field `isSelected`.
`void`	`setIUS(SortedSet<IUS> ius)` setIUS.
`void`	`setLanes(SortedSet<Lane> lanes)` Setter for the field `lanes`.
`void`	`setLanesForView(SortedSet<Lane> lanes)` setLanesForView.
`void`	`setName(String name)` Setter for the field `name`.
`void`	`setOrganism(Organism organism)` Setter for the field `organism`.
`void`	`setOrganismId(Integer organismId)` Setter for the field `organismId`.
`void`	`setOwner(Registration owner)` Setter for the field `owner`.
`void`	`setParents(Set<Sample> parents)` Setter for the field `parents`.
`void`	`setProcessings(Set<Processing> processings)` Setter for the field `processings`.
`void`	`setRegions(String regions)` Setter for the field `regions`.
`void`	`setSampleAttributes(Set<SampleAttribute> sampleAttributes)` Setter for the field `sampleAttributes`.
`void`	`setSampleId(Integer sampleId)` Setter for the field `sampleId`.
`void`	`setSkip(Boolean skip)` Setter for the field `skip`.
`void`	`setStrExpectedNumReads(String strExpectedNumReads)` Setter for the field `strExpectedNumReads`.
`void`	`setStrExpectedNumRuns(String strExpectedNumRuns)` Setter for the field `strExpectedNumRuns`.
`void`	`setSwAccession(Integer swAccession)` Setter for the field `swAccession`.
`void`	`setTags(String tags)` Setter for the field `tags`.
`void`	`setTitle(String title)` Setter for the field `title`.
`void`	`setType(String type)` Setter for the field `type`.
`void`	`setUpdateTimestamp(Date updateTimestamp)` Setter for the field `updateTimestamp`.
`String`	`toString()`

Methods inherited from class net.sourceforge.seqware.common.security.PermissionsAware
givesPermission, givesPermission

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

- Field Detail
  - GEO_REACTION_ID_ATTR_TAG
```
public static final String GEO_REACTION_ID_ATTR_TAG
```
    The presence of this attribute is used to identify that the sample is a library
    
    See Also:
    Constant Field Values
- Constructor Detail
  - Sample
```
public Sample()
```
    Constructor for Sample.
- Method Detail
  - compareTo
```
public int compareTo(Sample that)
```
    Specified by:
    
    compareTo in interface Comparable<Sample>
    
    Parameters:
    that -
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - equals
```
public boolean equals(Object other)
```
    Overrides:
    
    equals in class Object
    
    Parameters:
    other -
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - getAlias
```
public String getAlias()
```
    Getter for the field alias.
    
    Returns:
    a String object.
  - setAlias
```
public void setAlias(String alias)
```
    Setter for the field alias.
    
    Parameters:
    alias - a String object.
  - getOrganismId
```
public Integer getOrganismId()
```
    Getter for the field organismId.
    
    Returns:
    a Integer object.
  - setOrganismId
```
public void setOrganismId(Integer organismId)
```
    Setter for the field organismId.
    
    Parameters:
    organismId - a Integer object.
  - getAdapters
```
public String getAdapters()
```
    Getter for the field adapters.
    
    Returns:
    a String object.
  - setAdapters
```
public void setAdapters(String adapters)
```
    Setter for the field adapters.
    
    Parameters:
    adapters - a String object.
  - getIndividualName
```
public String getIndividualName()
```
    Getter for the field individualName.
    
    Returns:
    a String object.
  - setIndividualName
```
public void setIndividualName(String individualName)
```
    Setter for the field individualName.
    
    Parameters:
    individualName - a String object.
  - getTitle
```
public String getTitle()
```
    Getter for the field title.
    
    Returns:
    a String object.
  - getJsonEscapeTitle
```
public String getJsonEscapeTitle()
```
    getJsonEscapeTitle.
    
    Returns:
    a String object.
  - setTitle
```
public void setTitle(String title)
```
    Setter for the field title.
    
    Parameters:
    title - a String object.
  - getExpectedNumRuns
```
public Integer getExpectedNumRuns()
```
    Getter for the field expectedNumRuns.
    
    Returns:
    a Integer object.
  - setExpectedNumRuns
```
public void setExpectedNumRuns(Integer expectedNumRuns)
```
    Setter for the field expectedNumRuns.
    
    Parameters:
    expectedNumRuns - a Integer object.
  - getExpectedNumSpots
```
public Integer getExpectedNumSpots()
```
    Getter for the field expectedNumSpots.
    
    Returns:
    a Integer object.
  - setExpectedNumSpots
```
public void setExpectedNumSpots(Integer expectedNumSpots)
```
    Setter for the field expectedNumSpots.
    
    Parameters:
    expectedNumSpots - a Integer object.
  - getExpectedNumReads
```
public Integer getExpectedNumReads()
```
    Getter for the field expectedNumReads.
    
    Returns:
    a Integer object.
  - setExpectedNumReads
```
public void setExpectedNumReads(Integer expectedNumReads)
```
    Setter for the field expectedNumReads.
    
    Parameters:
    expectedNumReads - a Integer object.
  - getLanes
```
public SortedSet<Lane> getLanes()
```
    Getter for the field lanes.
    
    Returns:
    a SortedSet object.
  - setLanes
```
public void setLanes(SortedSet<Lane> lanes)
```
    Setter for the field lanes.
    
    Parameters:
    lanes - a SortedSet object.
  - setLanesForView
```
public void setLanesForView(SortedSet<Lane> lanes)
```
    setLanesForView.
    
    Parameters:
    lanes - a SortedSet object.
  - getSampleId
```
public Integer getSampleId()
```
    Getter for the field sampleId.
    
    Returns:
    a Integer object.
  - setSampleId
```
public void setSampleId(Integer sampleId)
```
    Setter for the field sampleId.
    
    Parameters:
    sampleId - a Integer object.
  - getExperiment
```
public Experiment getExperiment()
```
    Getter for the field experiment.
    
    Returns:
    a Experiment object.
  - setExperiment
```
public void setExperiment(Experiment experiment)
```
    Setter for the field experiment.
    
    Parameters:
    experiment - a Experiment object.
  - getOwner
```
public Registration getOwner()
```
    Getter for the field owner.
    
    Returns:
    a Registration object.
  - setOwner
```
public void setOwner(Registration owner)
```
    Setter for the field owner.
    
    Parameters:
    owner - a Registration object.
  - getAnonymizedName
```
public String getAnonymizedName()
```
    Getter for the field anonymizedName.
    
    Returns:
    a String object.
  - setAnonymizedName
```
public void setAnonymizedName(String anonymizedName)
```
    Setter for the field anonymizedName.
    
    Parameters:
    anonymizedName - a String object.
  - getName
```
public String getName()
```
    Getter for the field name.
    
    Returns:
    a String object.
  - getJsonEscapeName
```
public String getJsonEscapeName()
```
    getJsonEscapeName.
    
    Returns:
    a String object.
  - setName
```
public void setName(String name)
```
    Setter for the field name.
    
    Parameters:
    name - a String object.
  - getJsonEscapeDescription
```
public String getJsonEscapeDescription()
```
    getJsonEscapeDescription.
    
    Returns:
    a String object.
  - getDescription
```
public String getDescription()
```
    Getter for the field description.
    
    Returns:
    a String object.
  - setDescription
```
public void setDescription(String description)
```
    Setter for the field description.
    
    Parameters:
    description - a String object.
  - getType
```
public String getType()
```
    Getter for the field type.
    
    Returns:
    a String object.
  - setType
```
public void setType(String type)
```
    Setter for the field type.
    
    Parameters:
    type - a String object.
  - getTags
```
public String getTags()
```
    Getter for the field tags.
    
    Returns:
    a String object.
  - setTags
```
public void setTags(String tags)
```
    Setter for the field tags.
    
    Parameters:
    tags - a String object.
  - getRegions
```
public String getRegions()
```
    Getter for the field regions.
    
    Returns:
    a String object.
  - setRegions
```
public void setRegions(String regions)
```
    Setter for the field regions.
    
    Parameters:
    regions - a String object.
  - getSkip
```
public Boolean getSkip()
```
    Getter for the field skip.
    
    Returns:
    a Boolean object.
  - setSkip
```
public void setSkip(Boolean skip)
```
    Setter for the field skip.
    
    Parameters:
    skip - a Boolean object.
  - getCreateTimestamp
```
public Date getCreateTimestamp()
```
    Getter for the field createTimestamp.
    
    Returns:
    a Date object.
  - setCreateTimestamp
```
public void setCreateTimestamp(Date createTimestamp)
```
    Setter for the field createTimestamp.
    
    Parameters:
    createTimestamp - a Date object.
  - getUpdateTimestamp
```
public Date getUpdateTimestamp()
```
    Getter for the field updateTimestamp.
    
    Returns:
    a Date object.
  - setUpdateTimestamp
```
public void setUpdateTimestamp(Date updateTimestamp)
```
    Setter for the field updateTimestamp.
    
    Parameters:
    updateTimestamp - a Date object.
  - getSerialVersionUID
```
public static long getSerialVersionUID()
```
    Getter for the field serialVersionUID.
    
    Returns:
    a long.
  - getSwAccession
```
public Integer getSwAccession()
```
    Getter for the field swAccession.
    
    Specified by:
    
    getSwAccession in interface FirstTierModel
    
    Returns:
    a Integer object.
  - setSwAccession
```
public void setSwAccession(Integer swAccession)
```
    Setter for the field swAccession.
    
    Parameters:
    swAccession - a Integer object.
  - getOrganism
```
public Organism getOrganism()
```
    Getter for the field organism.
    
    Returns:
    a Organism object.
  - setOrganism
```
public void setOrganism(Organism organism)
```
    Setter for the field organism.
    
    Parameters:
    organism - a Organism object.
  - getIsSelected
```
public Boolean getIsSelected()
```
    Getter for the field isSelected.
    
    Returns:
    a Boolean object.
  - setIsSelected
```
public void setIsSelected(Boolean isSelected)
```
    Setter for the field isSelected.
    
    Parameters:
    isSelected - a Boolean object.
  - getIsHasFile
```
public Boolean getIsHasFile()
```
    Getter for the field isHasFile.
    
    Returns:
    a Boolean object.
  - setIsHasFile
```
public void setIsHasFile(Boolean isHasFile)
```
    Setter for the field isHasFile.
    
    Parameters:
    isHasFile - a Boolean object.
  - getCountFile
```
public Integer getCountFile()
```
    Getter for the field countFile.
    
    Returns:
    a Integer object.
  - setCountFile
```
public void setCountFile(Integer countFile)
```
    Setter for the field countFile.
    
    Parameters:
    countFile - a Integer object.
  - getStrExpectedNumRuns
```
public String getStrExpectedNumRuns()
```
    Getter for the field strExpectedNumRuns.
    
    Returns:
    a String object.
  - setStrExpectedNumRuns
```
public void setStrExpectedNumRuns(String strExpectedNumRuns)
```
    Setter for the field strExpectedNumRuns.
    
    Parameters:
    strExpectedNumRuns - a String object.
  - getStrExpectedNumReads
```
public String getStrExpectedNumReads()
```
    Getter for the field strExpectedNumReads.
    
    Returns:
    a String object.
  - setStrExpectedNumReads
```
public void setStrExpectedNumReads(String strExpectedNumReads)
```
    Setter for the field strExpectedNumReads.
    
    Parameters:
    strExpectedNumReads - a String object.
  - getIUS
```
public SortedSet<IUS> getIUS()
```
    getIUS.
    
    Returns:
    a SortedSet object.
  - setIUS
```
public void setIUS(SortedSet<IUS> ius)
```
    setIUS.
    
    Parameters:
    ius - a SortedSet object.
  - getProcessings
```
public Set<Processing> getProcessings()
```
    Getter for the field processings.
    
    Returns:
    a Set object.
  - setProcessings
```
public void setProcessings(Set<Processing> processings)
```
    Setter for the field processings.
    
    Parameters:
    processings - a Set object.
  - getParents
```
public Set<Sample> getParents()
```
    Getter for the field parents.
    
    Returns:
    a Set object.
  - setParents
```
public void setParents(Set<Sample> parents)
```
    Setter for the field parents.
    
    Parameters:
    parents - a Set object.
  - getChildren
```
public Set<Sample> getChildren()
```
    Getter for the field children.
    
    Returns:
    a Set object.
  - setChildren
```
public void setChildren(Set<Sample> children)
```
    Setter for the field children.
    
    Parameters:
    children - a Set object.
  - getSampleAttributes
```
public Set<SampleAttribute> getSampleAttributes()
```
    Getter for the field sampleAttributes.
    
    Returns:
    a Set object.
  - setSampleAttributes
```
public void setSampleAttributes(Set<SampleAttribute> sampleAttributes)
```
    Setter for the field sampleAttributes.
    
    Parameters:
    sampleAttributes - a Set object.
  - givesPermissionInternal
```
public boolean givesPermissionInternal(Registration registration,
                              Set<Integer> considered)
```
    Short-circuit permission checking by providing a set of entities that have already been checked
    
    Specified by:
    
    givesPermissionInternal in class PermissionsAware
    
    Returns:
  - getAnnotations
```
public Set<SampleAttribute> getAnnotations()
```
    Description copied from interface: Annotatable
    
    Get the annotations for this model
    
    Specified by:
    
    getAnnotations in interface Annotatable<SampleAttribute>
    
    Returns:

Class Sample

Field Summary

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.common.security.PermissionsAware

Methods inherited from class java.lang.Object

Field Detail

GEO_REACTION_ID_ATTR_TAG

Constructor Detail

Sample

Method Detail

compareTo

toString

equals

hashCode

getAlias

setAlias

getOrganismId

setOrganismId

getAdapters

setAdapters

getIndividualName

setIndividualName

getTitle

getJsonEscapeTitle

setTitle

getExpectedNumRuns

setExpectedNumRuns

getExpectedNumSpots

setExpectedNumSpots

getExpectedNumReads

setExpectedNumReads

getLanes

setLanes

setLanesForView

getSampleId

setSampleId

getExperiment

setExperiment

getOwner

setOwner

getAnonymizedName

setAnonymizedName

getName

getJsonEscapeName

setName

getJsonEscapeDescription

getDescription

setDescription

getType

setType

getTags

setTags

getRegions

setRegions

getSkip

setSkip

getCreateTimestamp

setCreateTimestamp

getUpdateTimestamp

setUpdateTimestamp

getSerialVersionUID

getSwAccession

setSwAccession

getOrganism

setOrganism

getIsSelected

setIsSelected

getIsHasFile

setIsHasFile

getCountFile

setCountFile

getStrExpectedNumRuns

setStrExpectedNumRuns

getStrExpectedNumReads

setStrExpectedNumReads

getIUS

setIUS

getProcessings

setProcessings