SequencerRun (SeqWare 1.1.2 API)

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

All Implemented Interfaces:

Serializable, Comparable<SequencerRun>, Annotatable<SequencerRunAttribute>, FirstTierModel, ParentAccessionModel

Direct Known Subclasses:

SequencerRunWizardDTO
```
public class SequencerRun
extends PermissionsAware
implements Serializable, Comparable<SequencerRun>, ParentAccessionModel, Annotatable<SequencerRunAttribute>, FirstTierModel
```
See Also:
Serialized Form

Constructor Summary

Constructors
Constructor and Description

SequencerRun()
Constructor for SequencerRun.

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

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(SequencerRun that)`
`boolean`	`equals(Object other)`
`Set<Processing>`	`getAllProcessing()` getAllProcessing.
`Set<SequencerRunAttribute>`	`getAnnotations()` Get the annotations for this model
`String`	`getColorMatrix()` Getter for the field `colorMatrix`.
`String`	`getColorMatrixCode()` Getter for the field `colorMatrixCode`.
`Date`	`getCreateTimestamp()` Getter for the field `createTimestamp`.
`Integer`	`getCycleCount()` Getter for the field `cycleCount`.
`String`	`getCycleDescriptor()` Getter for the field `cycleDescriptor`.
`String`	`getCycles()` Getter for the field `cycles`.
`String`	`getCycleSequence()` Getter for the field `cycleSequence`.
`String`	`getDescription()` Getter for the field `description`.
`int`	`getErrorCnt()` getErrorCnt.
`Integer`	`getErrorCount()` Getter for the field `errorCount`.
`String`	`getFilePath()` Getter for the field `filePath`.
`Integer`	`getFlowCount()` Getter for the field `flowCount`.
`String`	`getFlowSequence()` Getter for the field `flowSequence`.
`String`	`getHtml()` Getter for the field `html`.
`String`	`getInstrumentName()` Getter for the field `instrumentName`.
`String`	`getJsonEscapeDescription()` getJsonEscapeDescription.
`String`	`getJsonEscapeName()` getJsonEscapeName.
`SortedSet<Lane>`	`getLanes()` Getter for the field `lanes`.
`String`	`getName()` Getter for the field `name`.
`Registration`	`getOwner()` Getter for the field `owner`.
`Boolean`	`getPairedEnd()` Getter for the field `pairedEnd`.
`String`	`getPairedFilePath()` Getter for the field `pairedFilePath`.
`Platform`	`getPlatform()` Getter for the field `platform`.
`int`	`getPlatformInt()` Getter for the field `platformInt`.
`boolean`	`getProcess()` Getter for the field `process`.
`int`	`getProcessedCnt()` getProcessedCnt.
`Integer`	`getProcessedCount()` Getter for the field `processedCount`.
`int`	`getProcessingCnt()` getProcessingCnt.
`Integer`	`getProcessingCount()` Getter for the field `processingCount`.
`Set<Processing>`	`getProcessings()` Getter for the field `processings`.
`Integer`	`getRefLane()` Getter for the field `refLane`.
`String`	`getRunCenter()` Getter for the field `runCenter`.
`Set<SequencerRunAttribute>`	`getSequencerRunAttributes()` Getter for the field `sequencerRunAttributes`.
`Integer`	`getSequencerRunId()` Getter for the field `sequencerRunId`.
`static long`	`getSerialVersionUID()` Getter for the field `serialVersionUID`.
`Boolean`	`getSkip()` Getter for the field `skip`.
`String`	`getSlideOneFilePath()` Getter for the field `slideOneFilePath`.
`Integer`	`getSlideOneLaneCount()` Getter for the field `slideOneLaneCount`.
`String`	`getSlideTwoFilePath()` Getter for the field `slideTwoFilePath`.
`Integer`	`getSlideTwoLaneCount()` Getter for the field `slideTwoLaneCount`.
`SequencerRunStatus`	`getStatus()` Getter for the field `status`.
`String`	`getStrRefLane()` Getter for the field `strRefLane`.
`Integer`	`getSwAccession()` Getter for the field `swAccession`.
`Date`	`getUpdateTimestamp()` Getter for the field `updateTimestamp`.
`Boolean`	`getUseIparIntensities()` Getter for the field `useIparIntensities`.
`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`	`setColorMatrix(String colorMatrix)` Setter for the field `colorMatrix`.
`void`	`setColorMatrixCode(String colorMatrixCode)` Setter for the field `colorMatrixCode`.
`void`	`setCreateTimestamp(Date createTimestamp)` Setter for the field `createTimestamp`.
`void`	`setCycleCount(Integer cycleCount)` Setter for the field `cycleCount`.
`void`	`setCycleDescriptor(String cycleDescriptor)` Setter for the field `cycleDescriptor`.
`void`	`setCycles(String cycles)` Setter for the field `cycles`.
`void`	`setCycleSequence(String cycleSequence)` Setter for the field `cycleSequence`.
`void`	`setDescription(String description)` Setter for the field `description`.
`void`	`setErrorCount(Integer errorCount)` Setter for the field `errorCount`.
`void`	`setFilePath(String filePath)` Setter for the field `filePath`.
`void`	`setFlowCount(Integer flowCount)` Setter for the field `flowCount`.
`void`	`setFlowSequence(String flowSequence)` Setter for the field `flowSequence`.
`void`	`setHtml(String html)` Setter for the field `html`.
`void`	`setInstrumentName(String instrumentName)` Setter for the field `instrumentName`.
`void`	`setLanes(SortedSet<Lane> lanes)` Setter for the field `lanes`.
`void`	`setName(String name)` Setter for the field `name`.
`void`	`setOwner(Registration owner)` Setter for the field `owner`.
`void`	`setPairedEnd(Boolean pairedEnd)` Setter for the field `pairedEnd`.
`void`	`setPairedFilePath(String pairedFilePath)` Setter for the field `pairedFilePath`.
`void`	`setPlatform(Platform platform)` Setter for the field `platform`.
`void`	`setPlatformInt(int platformInt)` Setter for the field `platformInt`.
`void`	`setProcess(Boolean process)` Setter for the field `process`.
`void`	`setProcessedCount(Integer processedCount)` Setter for the field `processedCount`.
`void`	`setProcessingCount(Integer processingCount)` Setter for the field `processingCount`.
`void`	`setProcessings(Set<Processing> processings)` Setter for the field `processings`.
`void`	`setRefLane(Integer refLane)` Setter for the field `refLane`.
`void`	`setRunCenter(String runCenter)` Setter for the field `runCenter`.
`void`	`setSequencerRunAttributes(Set<SequencerRunAttribute> sequencerRunAttributes)` Setter for the field `sequencerRunAttributes`.
`void`	`setSequencerRunId(Integer sequencerRunId)` Setter for the field `sequencerRunId`.
`void`	`setSkip(Boolean skip)` Setter for the field `skip`.
`void`	`setSlideOneFilePath(String slideOneFilePath)` Setter for the field `slideOneFilePath`.
`void`	`setSlideOneLaneCount(Integer slideOneLaneCount)` Setter for the field `slideOneLaneCount`.
`void`	`setSlideTwoFilePath(String slideTwoFilePath)` Setter for the field `slideTwoFilePath`.
`void`	`setSlideTwoLaneCount(Integer slideTwoLaneCount)` Setter for the field `slideTwoLaneCount`.
`void`	`setStatus(SequencerRunStatus status)` Setter for the field `status`.
`void`	`setStrRefLane(String strRefLane)` Setter for the field `strRefLane`.
`void`	`setSwAccession(Integer swAccession)` Setter for the field `swAccession`.
`void`	`setUpdateTimestamp(Date updateTimestamp)` Setter for the field `updateTimestamp`.
`void`	`setUseIparIntensities(Boolean useIparIntensities)` Setter for the field `useIparIntensities`.
`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
  - SequencerRun
```
public SequencerRun()
```
    Constructor for SequencerRun.
- Method Detail
  - compareTo
```
public int compareTo(SequencerRun that)
```
    Specified by:
    
    compareTo in interface Comparable<SequencerRun>
    
    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
  - getAllProcessing
```
public Set<Processing> getAllProcessing()
```
    getAllProcessing.
    
    Returns:
    a Set 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.
  - getProcess
```
public boolean getProcess()
```
    Getter for the field process.
    
    Returns:
    a Boolean object.
  - setProcess
```
public void setProcess(Boolean process)
```
    Setter for the field process.
    
    Parameters:
    process - a Boolean 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.
  - getSequencerRunId
```
public Integer getSequencerRunId()
```
    Getter for the field sequencerRunId.
    
    Returns:
    a Integer object.
  - setSequencerRunId
```
public void setSequencerRunId(Integer sequencerRunId)
```
    Setter for the field sequencerRunId.
    
    Parameters:
    sequencerRunId - a Integer object.
  - getSerialVersionUID
```
public static long getSerialVersionUID()
```
    Getter for the field serialVersionUID.
    
    Returns:
    a long.
  - 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.
  - getCycles
```
public String getCycles()
```
    Getter for the field cycles.
    
    Returns:
    a String object.
  - setCycles
```
public void setCycles(String cycles)
```
    Setter for the field cycles.
    
    Parameters:
    cycles - 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.
  - getFilePath
```
public String getFilePath()
```
    Getter for the field filePath.
    
    Returns:
    a String object.
  - setFilePath
```
public void setFilePath(String filePath)
```
    Setter for the field filePath.
    
    Parameters:
    filePath - a String object.
  - getRefLane
```
public Integer getRefLane()
```
    Getter for the field refLane.
    
    Returns:
    a Integer object.
  - setRefLane
```
public void setRefLane(Integer refLane)
```
    Setter for the field refLane.
    
    Parameters:
    refLane - a Integer object.
  - getStatus
```
public SequencerRunStatus getStatus()
```
    Getter for the field status.
    
    Returns:
    a String object.
  - setStatus
```
public void setStatus(SequencerRunStatus status)
```
    Setter for the field status.
    
    Parameters:
    status - a String 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.
  - 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.
  - 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.
  - 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.
  - getPairedEnd
```
public Boolean getPairedEnd()
```
    Getter for the field pairedEnd.
    
    Returns:
    a Boolean object.
  - setPairedEnd
```
public void setPairedEnd(Boolean pairedEnd)
```
    Setter for the field pairedEnd.
    
    Parameters:
    pairedEnd - a Boolean object.
  - getPairedFilePath
```
public String getPairedFilePath()
```
    Getter for the field pairedFilePath.
    
    Returns:
    a String object.
  - setPairedFilePath
```
public void setPairedFilePath(String pairedFilePath)
```
    Setter for the field pairedFilePath.
    
    Parameters:
    pairedFilePath - a String object.
  - getUseIparIntensities
```
public Boolean getUseIparIntensities()
```
    Getter for the field useIparIntensities.
    
    Returns:
    a Boolean object.
  - setUseIparIntensities
```
public void setUseIparIntensities(Boolean useIparIntensities)
```
    Setter for the field useIparIntensities.
    
    Parameters:
    useIparIntensities - a Boolean 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.
  - getPlatform
```
public Platform getPlatform()
```
    Getter for the field platform.
    
    Returns:
    a Platform object.
  - setPlatform
```
public void setPlatform(Platform platform)
```
    Setter for the field platform.
    
    Parameters:
    platform - a Platform object.
  - getInstrumentName
```
public String getInstrumentName()
```
    Getter for the field instrumentName.
    
    Returns:
    a String object.
  - setInstrumentName
```
public void setInstrumentName(String instrumentName)
```
    Setter for the field instrumentName.
    
    Parameters:
    instrumentName - a String 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.
  - getCycleSequence
```
public String getCycleSequence()
```
    Getter for the field cycleSequence.
    
    Returns:
    a String object.
  - setCycleSequence
```
public void setCycleSequence(String cycleSequence)
```
    Setter for the field cycleSequence.
    
    Parameters:
    cycleSequence - a String object.
  - getCycleCount
```
public Integer getCycleCount()
```
    Getter for the field cycleCount.
    
    Returns:
    a Integer object.
  - setCycleCount
```
public void setCycleCount(Integer cycleCount)
```
    Setter for the field cycleCount.
    
    Parameters:
    cycleCount - a Integer object.
  - getColorMatrix
```
public String getColorMatrix()
```
    Getter for the field colorMatrix.
    
    Returns:
    a String object.
  - setColorMatrix
```
public void setColorMatrix(String colorMatrix)
```
    Setter for the field colorMatrix.
    
    Parameters:
    colorMatrix - a String object.
  - getColorMatrixCode
```
public String getColorMatrixCode()
```
    Getter for the field colorMatrixCode.
    
    Returns:
    a String object.
  - setColorMatrixCode
```
public void setColorMatrixCode(String colorMatrixCode)
```
    Setter for the field colorMatrixCode.
    
    Parameters:
    colorMatrixCode - a String object.
  - getSlideOneLaneCount
```
public Integer getSlideOneLaneCount()
```
    Getter for the field slideOneLaneCount.
    
    Returns:
    a Integer object.
  - setSlideOneLaneCount
```
public void setSlideOneLaneCount(Integer slideOneLaneCount)
```
    Setter for the field slideOneLaneCount.
    
    Parameters:
    slideOneLaneCount - a Integer object.
  - getSlideTwoLaneCount
```
public Integer getSlideTwoLaneCount()
```
    Getter for the field slideTwoLaneCount.
    
    Returns:
    a Integer object.
  - setSlideTwoLaneCount
```
public void setSlideTwoLaneCount(Integer slideTwoLaneCount)
```
    Setter for the field slideTwoLaneCount.
    
    Parameters:
    slideTwoLaneCount - a Integer object.
  - getSlideOneFilePath
```
public String getSlideOneFilePath()
```
    Getter for the field slideOneFilePath.
    
    Returns:
    a String object.
  - setSlideOneFilePath
```
public void setSlideOneFilePath(String slideOneFilePath)
```
    Setter for the field slideOneFilePath.
    
    Parameters:
    slideOneFilePath - a String object.
  - getSlideTwoFilePath
```
public String getSlideTwoFilePath()
```
    Getter for the field slideTwoFilePath.
    
    Returns:
    a String object.
  - setSlideTwoFilePath
```
public void setSlideTwoFilePath(String slideTwoFilePath)
```
    Setter for the field slideTwoFilePath.
    
    Parameters:
    slideTwoFilePath - a String object.
  - getFlowSequence
```
public String getFlowSequence()
```
    Getter for the field flowSequence.
    
    Returns:
    a String object.
  - setFlowSequence
```
public void setFlowSequence(String flowSequence)
```
    Setter for the field flowSequence.
    
    Parameters:
    flowSequence - a String object.
  - getFlowCount
```
public Integer getFlowCount()
```
    Getter for the field flowCount.
    
    Returns:
    a Integer object.
  - setFlowCount
```
public void setFlowCount(Integer flowCount)
```
    Setter for the field flowCount.
    
    Parameters:
    flowCount - a Integer object.
  - getRunCenter
```
public String getRunCenter()
```
    Getter for the field runCenter.
    
    Returns:
    a String object.
  - setRunCenter
```
public void setRunCenter(String runCenter)
```
    Setter for the field runCenter.
    
    Parameters:
    runCenter - a String object.
  - getPlatformInt
```
public int getPlatformInt()
```
    Getter for the field platformInt.
    
    Returns:
    a int.
  - setPlatformInt
```
public void setPlatformInt(int platformInt)
```
    Setter for the field platformInt.
    
    Parameters:
    platformInt - a int.
  - getJsonEscapeDescription
```
public String getJsonEscapeDescription()
```
    getJsonEscapeDescription.
    
    Returns:
    a String object.
  - getProcessingCount
```
public Integer getProcessingCount()
```
    Getter for the field processingCount.
    
    Returns:
    a Integer object.
  - setProcessingCount
```
public void setProcessingCount(Integer processingCount)
```
    Setter for the field processingCount.
    
    Parameters:
    processingCount - a Integer object.
  - getProcessedCount
```
public Integer getProcessedCount()
```
    Getter for the field processedCount.
    
    Returns:
    a Integer object.
  - setProcessedCount
```
public void setProcessedCount(Integer processedCount)
```
    Setter for the field processedCount.
    
    Parameters:
    processedCount - a Integer object.
  - getErrorCount
```
public Integer getErrorCount()
```
    Getter for the field errorCount.
    
    Returns:
    a Integer object.
  - setErrorCount
```
public void setErrorCount(Integer errorCount)
```
    Setter for the field errorCount.
    
    Parameters:
    errorCount - a Integer object.
  - getHtml
```
public String getHtml()
```
    Getter for the field html.
    
    Returns:
    a String object.
  - setHtml
```
public void setHtml(String html)
```
    Setter for the field html.
    
    Parameters:
    html - a String object.
  - getStrRefLane
```
public String getStrRefLane()
```
    Getter for the field strRefLane.
    
    Returns:
    a String object.
  - setStrRefLane
```
public void setStrRefLane(String strRefLane)
```
    Setter for the field strRefLane.
    
    Parameters:
    strRefLane - 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.
  - getSequencerRunAttributes
```
public Set<SequencerRunAttribute> getSequencerRunAttributes()
```
    Getter for the field sequencerRunAttributes.
    
    Returns:
    a Set object.
  - setSequencerRunAttributes
```
public void setSequencerRunAttributes(Set<SequencerRunAttribute> sequencerRunAttributes)
```
    Setter for the field sequencerRunAttributes.
    
    Parameters:
    sequencerRunAttributes - 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<SequencerRunAttribute> getAnnotations()
```
    Description copied from interface: Annotatable
    
    Get the annotations for this model
    
    Specified by:
    
    getAnnotations in interface Annotatable<SequencerRunAttribute>
    
    Returns:

Class SequencerRun

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

SequencerRun

Method Detail

compareTo

toString

equals

hashCode

getAllProcessing

getErrorCnt

getProcessingCnt

getProcessedCnt

getProcess

setProcess

getSwAccession

setSwAccession

getSequencerRunId

setSequencerRunId

getSerialVersionUID

getCreateTimestamp

setCreateTimestamp

getCycles

setCycles

getDescription

setDescription

getFilePath

setFilePath

getRefLane

setRefLane

getStatus

setStatus

getUpdateTimestamp

setUpdateTimestamp

getName

getJsonEscapeName

setName

getProcessings

setProcessings

getLanes

setLanes

getPairedEnd

setPairedEnd

getPairedFilePath

setPairedFilePath

getUseIparIntensities

setUseIparIntensities

getOwner

setOwner

getPlatform

setPlatform

getInstrumentName

setInstrumentName

getCycleDescriptor

setCycleDescriptor

getCycleSequence

setCycleSequence

getCycleCount

setCycleCount

getColorMatrix

setColorMatrix

getColorMatrixCode

setColorMatrixCode

getSlideOneLaneCount

setSlideOneLaneCount

getSlideTwoLaneCount

setSlideTwoLaneCount

getSlideOneFilePath

setSlideOneFilePath

getSlideTwoFilePath

setSlideTwoFilePath

getFlowSequence

setFlowSequence

getFlowCount

setFlowCount

getRunCenter

setRunCenter