Lane (SeqWare 1.1.2 API)

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

All Implemented Interfaces:: Serializable, Comparable<Lane>, Annotatable<LaneAttribute>, FirstTierModel, ParentAccessionModel

public class Lane
extends PermissionsAware
implements Serializable, Comparable<Lane>, ParentAccessionModel, Annotatable<LaneAttribute>, FirstTierModel

See Also:: Serialized Form

Constructor Summary

Constructors
Constructor and Description

Lane()
Constructor for Lane.

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addProcessing(Processing processing)` addProcessing.
`int`	`compareTo(Lane that)`
`boolean`	`equals(Object other)`
`Set<Processing>`	`getAllProcessings()` getAllProcessings.
`Set<LaneAttribute>`	`getAnnotations()` Get the annotations for this model
`Date`	`getCreateTimestamp()` Getter for the field `createTimestamp`.
`String`	`getCycleDescriptor()` Getter for the field `cycleDescriptor`.
`String`	`getDescription()` Getter for the field `description`.
`int`	`getErrorCnt()` getErrorCnt.
`Boolean`	`getIsHasFile()` Getter for the field `isHasFile`.
`Boolean`	`getIsSelected()` Getter for the field `isSelected`.
`SortedSet<IUS>`	`getIus()` Getter for the field `ius`.
`SortedSet<IUS>`	`getIUS()` getIUS.
`String`	`getJsonEscapeDescription()` getJsonEscapeDescription.
`String`	`getJsonEscapeName()` getJsonEscapeName.
`Set<LaneAttribute>`	`getLaneAttributes()` Getter for the field `laneAttributes`.
`Integer`	`getLaneId()` Getter for the field `laneId`.
`Integer`	`getLaneIndex()` Getter for the field `laneIndex`.
`LibrarySelection`	`getLibrarySelection()`
`LibrarySource`	`getLibrarySource()`
`LibraryStrategy`	`getLibraryStrategy()`
`String`	`getName()` Getter for the field `name`.
`String`	`getOrganism()` Getter for the field `organism`.
`Registration`	`getOwner()` Getter for the field `owner`.
`int`	`getProcessedCnt()` getProcessedCnt.
`int`	`getProcessingCnt()` getProcessingCnt.
`Set<Processing>`	`getProcessings()` Getter for the field `processings`.
`String`	`getRegions()` Getter for the field `regions`.
`Sample`	`getSample()` Getter for the field `sample`.
`String`	`getSampleCode()` Getter for the field `sampleCode`.
`SortedSet<Sample>`	`getSamples()` getSamples.
`String`	`getSampleType()` Getter for the field `sampleType`.
`SequencerRun`	`getSequencerRun()` Getter for the field `sequencerRun`.
`static long`	`getSerialVersionUID()` Getter for the field `serialVersionUID`.
`Boolean`	`getSkip()` Getter for the field `skip`.
`StudyType`	`getStudyType()`
`Integer`	`getSwAccession()` Getter for the field `swAccession`.
`String`	`getTags()` Getter for the field `tags`.
`Date`	`getUpdateTimestamp()` Getter for the field `updateTimestamp`.
`Set<WorkflowRun>`	`getWorkflowRuns()` Getter for the field `workflowRuns`.
`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`	`setCreateTimestamp(Date createTimestamp)` Setter for the field `createTimestamp`.
`void`	`setCycleDescriptor(String cycleDescriptor)` Setter for the field `cycleDescriptor`.
`void`	`setDescription(String description)` Setter for the field `description`.
`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`	`setLaneAttributes(Set<LaneAttribute> laneAttributes)` Setter for the field `laneAttributes`.
`void`	`setLaneId(Integer laneId)` Setter for the field `laneId`.
`void`	`setLaneIndex(Integer laneIndex)` Setter for the field `laneIndex`.
`void`	`setLibrarySelection(LibrarySelection librarySelection)`
`void`	`setLibrarySource(LibrarySource librarySource)`
`void`	`setLibraryStrategy(LibraryStrategy libraryStrategy)`
`void`	`setName(String name)` Setter for the field `name`.
`void`	`setOrganism(String organism)` Setter for the field `organism`.
`void`	`setOwner(Registration owner)` Setter for the field `owner`.
`void`	`setProcessings(Set<Processing> processings)` Setter for the field `processings`.
`void`	`setProcessingsForView(Set<Processing> processings)` setProcessingsForView.
`void`	`setRegions(String regions)` Setter for the field `regions`.
`void`	`setSample(Sample sample)` Setter for the field `sample`.
`void`	`setSampleCode(String sampleCode)` Setter for the field `sampleCode`.
`void`	`setSampleType(String sampleType)` Setter for the field `sampleType`.
`void`	`setSequencerRun(SequencerRun sequencerRun)` Setter for the field `sequencerRun`.
`void`	`setSkip(Boolean skip)` Setter for the field `skip`.
`void`	`setStudyType(StudyType studyType)`
`void`	`setSwAccession(Integer swAccession)` Setter for the field `swAccession`.
`void`	`setTags(String tags)` Setter for the field `tags`.
`void`	`setUpdateTimestamp(Date updateTimestamp)` Setter for the field `updateTimestamp`.
`void`	`setWorkflowRuns(Set<WorkflowRun> workflowRuns)` Setter for the field `workflowRuns`.
`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

- Constructor Detail
  - Lane
```
public Lane()
```
    Constructor for Lane.
- Method Detail
  - compareTo
```
public int compareTo(Lane that)
```
    Specified by:
    
    compareTo in interface Comparable<Lane>
    
    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
  - getErrorCnt
```
public int getErrorCnt()
```
    getErrorCnt.
    
    Returns:
    a int.
  - getProcessingCnt
```
public int getProcessingCnt()
```
    getProcessingCnt.
    
    Returns:
    a int.
  - getProcessedCnt
```
public int getProcessedCnt()
```
    getProcessedCnt.
    
    Returns:
    a int.
  - getAllProcessings
```
public Set<Processing> getAllProcessings()
```
    getAllProcessings.
    
    Returns:
    a Set object.
  - getIus
```
public SortedSet<IUS> getIus()
```
    Getter for the field ius.
    
    Returns:
    a SortedSet object.
  - getIUS
```
public SortedSet<IUS> getIUS()
```
    getIUS.
    
    Returns:
    a SortedSet object.
  - setIUS
```
public void setIUS(SortedSet<IUS> ius)
```
    setIUS.
    
    Parameters:
    ius - a SortedSet object.
  - getLaneIndex
```
public Integer getLaneIndex()
```
    Getter for the field laneIndex.
    
    Returns:
    a Integer object.
  - setLaneIndex
```
public void setLaneIndex(Integer laneIndex)
```
    Setter for the field laneIndex.
    
    Parameters:
    laneIndex - a Integer object.
  - getCycleDescriptor
```
public String getCycleDescriptor()
```
    Getter for the field cycleDescriptor.
    
    Returns:
    a String object.
  - setCycleDescriptor
```
public void setCycleDescriptor(String cycleDescriptor)
```
    Setter for the field cycleDescriptor.
    
    Parameters:
    cycleDescriptor - a String object.
  - 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.
  - 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.
  - setProcessingsForView
```
public void setProcessingsForView(Set<Processing> processings)
```
    setProcessingsForView.
    
    Parameters:
    processings - a Set object.
  - addProcessing
```
public void addProcessing(Processing processing)
```
    addProcessing.
    
    Parameters:
    processing - a Processing object.
  - getSamples
```
public SortedSet<Sample> getSamples()
```
    getSamples.
    
    Returns:
    a SortedSet object.
  - getSample
```
public Sample getSample()
```
    Getter for the field sample.
    
    Returns:
    a Sample object.
  - setSample
```
public void setSample(Sample sample)
```
    Setter for the field sample.
    
    Parameters:
    sample - a Sample 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.
  - 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.
  - 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.
  - getLaneId
```
public Integer getLaneId()
```
    Getter for the field laneId.
    
    Returns:
    a Integer object.
  - setLaneId
```
public void setLaneId(Integer laneId)
```
    Setter for the field laneId.
    
    Parameters:
    laneId - a Integer 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.
  - getOrganism
```
public String getOrganism()
```
    Getter for the field organism.
    
    Returns:
    a String object.
  - setOrganism
```
public void setOrganism(String organism)
```
    Setter for the field organism.
    
    Parameters:
    organism - a String object.
  - getSampleType
```
public String getSampleType()
```
    Getter for the field sampleType.
    
    Returns:
    a String object.
  - setSampleType
```
public void setSampleType(String sampleType)
```
    Setter for the field sampleType.
    
    Parameters:
    sampleType - a String object.
  - getSampleCode
```
public String getSampleCode()
```
    Getter for the field sampleCode.
    
    Returns:
    a String object.
  - setSampleCode
```
public void setSampleCode(String sampleCode)
```
    Setter for the field sampleCode.
    
    Parameters:
    sampleCode - 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.
  - getSequencerRun
```
public SequencerRun getSequencerRun()
```
    Getter for the field sequencerRun.
    
    Returns:
    a SequencerRun object.
  - setSequencerRun
```
public void setSequencerRun(SequencerRun sequencerRun)
```
    Setter for the field sequencerRun.
    
    Parameters:
    sequencerRun - a SequencerRun 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.
  - 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.
  - getWorkflowRuns
```
public Set<WorkflowRun> getWorkflowRuns()
```
    Getter for the field workflowRuns.
    
    Returns:
    a Set object.
  - setWorkflowRuns
```
public void setWorkflowRuns(Set<WorkflowRun> workflowRuns)
```
    Setter for the field workflowRuns.
    
    Parameters:
    workflowRuns - a Set object.
  - getLaneAttributes
```
public Set<LaneAttribute> getLaneAttributes()
```
    Getter for the field laneAttributes.
    
    Returns:
    a Set object.
  - setLaneAttributes
```
public void setLaneAttributes(Set<LaneAttribute> laneAttributes)
```
    Setter for the field laneAttributes.
    
    Parameters:
    laneAttributes - a Set object.
  - givesPermissionInternal
```
public boolean givesPermissionInternal(Registration registration,
                              Set<Integer> considered)
```
    Description copied from class: PermissionsAware
    
    Short-circuit permission checking by providing a set of entities that have already been checked
    
    Specified by:
    
    givesPermissionInternal in class PermissionsAware
    
    Returns:
  - getStudyType
```
public StudyType getStudyType()
```
  - setStudyType
```
public void setStudyType(StudyType studyType)
```
  - getLibraryStrategy
```
public LibraryStrategy getLibraryStrategy()
```
  - setLibraryStrategy
```
public void setLibraryStrategy(LibraryStrategy libraryStrategy)
```
  - getLibrarySelection
```
public LibrarySelection getLibrarySelection()
```
  - setLibrarySelection
```
public void setLibrarySelection(LibrarySelection librarySelection)
```
  - getLibrarySource
```
public LibrarySource getLibrarySource()
```
  - setLibrarySource
```
public void setLibrarySource(LibrarySource librarySource)
```
  - getAnnotations
```
public Set<LaneAttribute> getAnnotations()
```
    Description copied from interface: Annotatable
    
    Get the annotations for this model
    
    Specified by:
    
    getAnnotations in interface Annotatable<LaneAttribute>
    
    Returns:

Class Lane

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

Lane

Method Detail

compareTo

toString

equals

hashCode

getErrorCnt

getProcessingCnt

getProcessedCnt

getAllProcessings

getIus

getIUS

setIUS

getLaneIndex

setLaneIndex

getCycleDescriptor

setCycleDescriptor

getSwAccession

setSwAccession

getProcessings

setProcessings

setProcessingsForView

addProcessing

getSamples

getSample

setSample

getCreateTimestamp

setCreateTimestamp

getUpdateTimestamp

setUpdateTimestamp

getSerialVersionUID

getJsonEscapeDescription

getDescription

setDescription

getTags

setTags

getRegions

setRegions

getLaneId

setLaneId

getName

getJsonEscapeName

setName

getOrganism

setOrganism

getSampleType

setSampleType

getSampleCode

setSampleCode

getSkip

setSkip

getSequencerRun

setSequencerRun

getOwner

setOwner

getIsSelected

setIsSelected

getIsHasFile

setIsHasFile

getWorkflowRuns

setWorkflowRuns

getLaneAttributes

setLaneAttributes

givesPermissionInternal

getStudyType

setStudyType

getLibraryStrategy

setLibraryStrategy

getLibrarySelection

setLibrarySelection

getLibrarySource

setLibrarySource

getAnnotations