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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
public class ExperimentBean
Holds all information regarding an experiment (sequencing trace). Many of the boolean fields are provided for use by the Velocity Template engine as null cannot be tested for in the return of a method (velocity assumes that the method does not exist if it returns null).
Constructor Summary | |
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ExperimentBean(uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface tdi)
Creates a new instance of ExperimentBean. |
Method Summary | |
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int |
compareTo(java.lang.Object o)
|
boolean |
equals(java.lang.Object o)
|
java.lang.String |
getAmplimerName()
Gets the amplimer name |
ExperimentBean |
getComplimentExp()
The ExperimentBean of any compliment experiment, requires correct use of runNumber for experiment pairing. |
java.lang.String |
getComplimentFileName()
The file name of any compliment experiment, requires correct use of runNumber for experiment pairing. |
uk.ac.sanger.cgp.autocsa.beans.CSAOutput |
getCompResult()
Get the result of a comparison. |
java.lang.Float |
getCsaSelectionScore()
Get csaSelectionScore . |
int |
getCsaSelectionScorePrim()
Get csaSelectionScore as a primitive int. |
uk.ac.sanger.cgp.autocsa.interfaces.CsaTraceInterface |
getCsaTrace()
Get the CsaTrace object. |
java.lang.String |
getDnaName()
Get the DNA/sample name. |
CsaError |
getError()
Get any CsaError that may have been handled during analysis. |
java.lang.Throwable |
getException()
Get any exception that may have been handled on the creation of a CsaError. |
java.lang.String |
getFileNoPath()
Returns the name of the file linked to this experiment with no path. |
java.lang.String |
getFileNoPathOrExtension()
Gets the filename with no path or extension. |
java.lang.Integer |
getRunNumber()
Get run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided. |
int |
getStrandPreFlaggingCountStatus()
Flagging parameter, here for convenience. |
uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface |
getTraceDetails()
Get the TraceDetails object |
java.lang.String |
getTraceStatus()
Textual description of the experiment status. |
java.lang.String |
getUniqueNameForFile()
Returns a unique name for a result. |
java.lang.String |
getUniqueNameForVariant()
Returns a unique name for a variant see setVariantToRender(Mutation variantToRender) . |
java.util.Map |
getVariantGroups()
Get the map of different classes of variant. |
uk.ac.sanger.cgp.autocsa.beans.Mutation |
getVariantToRender()
Get the current variant being rendered. |
int |
hashCode()
|
boolean |
isBest()
Applies to wildtype traces only, indicates if this is the current best wildtype experiment based on csaSelectionScore . |
boolean |
isCompared()
Indicates if the experiment has been used in a comparison. |
boolean |
isComplimentPresent()
Indicates that a compliment experiment is avilable, requires correct use of runNumber for experiment pairing. |
boolean |
isFlagAssessed()
True when flagging has been attempted on this experiment. |
boolean |
isOthersPresent()
Indicates when non-substitution variants are available. |
boolean |
isSense()
True when this experiment was sequenced in the sense direction (with respect to the amplimer sequence). |
boolean |
isSubsPresent()
Indicates when substitution variants are available. |
boolean |
isWildtype()
True when a wildtype experiment. |
void |
setAmplimerName(java.lang.String amplimerName)
Set the amplimerName to the provided string |
void |
setBest(boolean best)
Set this experiment as best. |
void |
setComplimentExp(ExperimentBean complimentExp)
Set the ExperimentBean of any compliment experiment, requires correct use of runNumber for experiment pairing. |
void |
setCompResult(uk.ac.sanger.cgp.autocsa.beans.CSAOutput compResult)
Set the CSAOutput, result of a comparison. |
void |
setCsaSelectionScore(java.lang.Float csaSelectionScore)
Set csaSelectionScore . |
void |
setCsaTrace(uk.ac.sanger.cgp.autocsa.interfaces.CsaTraceInterface csaTrace)
Set the CsaTrace object. |
void |
setDnaName(java.lang.String dnaName)
Set the dna name |
void |
setError(CsaError error)
Set any CsaError that may have been handled during analysis. |
void |
setError(CsaError error,
java.lang.Throwable exception)
Set any CsaError that may have been handled during analysis, along with any associated exception. |
void |
setFlagAssessed(boolean flagAssessed)
True when flagging has been attempted on this experiment. |
void |
setOthersPresent(boolean othersPresent)
Set indicator for when non-substitution variants are available. |
void |
setRunNumber(java.lang.Integer runNumber)
Set run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided. |
void |
setRunNumber(java.lang.String runNumber)
Set run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided. |
void |
setSense(char direction)
Set the sequencing direction with respect to the amplimer. |
void |
setStrandPreFlaggingCountStatus(int strandPreFlaggingCountStatus)
Flagging parameter, here for convenience. |
void |
setSubsPresent(boolean subsPresent)
Set indicator for when substitution variants are available. |
void |
setTraceDetails(uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface traceDetails)
Set the TraceDetails object |
void |
setTraceStatus(java.lang.String traceStatus)
Set a textual description of the experiment status. |
void |
setVariantToRender(uk.ac.sanger.cgp.autocsa.beans.Mutation variantToRender)
Set the variant to be rendered. |
void |
setWildtype(boolean wildtype)
Set the wildtype indicator |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ExperimentBean(uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface tdi)
tdi
- a TraceDetails object populated with filePositionFromRootMethod Detail |
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public java.lang.String getFileNoPathOrExtension()
public java.lang.String getAmplimerName()
public void setAmplimerName(java.lang.String amplimerName)
amplimerName
- the name of the amplimer associated with this experimentpublic java.lang.String getDnaName()
public void setDnaName(java.lang.String dnaName)
dnaName
- the name of the DNA/sample associated with this experimentpublic boolean isSense()
public void setSense(char direction)
direction
- f for sense/forward, r for antisense/reversepublic java.lang.String getUniqueNameForVariant()
setVariantToRender(Mutation variantToRender)
.
public java.lang.String getUniqueNameForFile()
getDnaName()
- getRunNumber()
- getTraceDetails()
.getForwardOrReverseStrand()
public java.lang.Integer getRunNumber()
public void setRunNumber(java.lang.String runNumber)
setRunNumber(Integer runNumber)
runNumber
- run number of this experimentpublic void setRunNumber(java.lang.Integer runNumber)
runNumber
- run number of this experimentpublic uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface getTraceDetails()
public void setTraceDetails(uk.ac.sanger.cgp.autocsa.interfaces.TraceDetailsInterface traceDetails)
traceDetails
- the TraceDetails objectpublic boolean isWildtype()
public void setWildtype(boolean wildtype)
wildtype
- true when wildtype sample/DNApublic java.lang.String getFileNoPath()
public CsaError getError()
public void setError(CsaError error)
error
- a CsaErrorpublic void setError(CsaError error, java.lang.Throwable exception)
error
- a CsaErrorexception
- any exception that was thrown when this type of CsaError was createdpublic java.lang.Throwable getException()
public int getCsaSelectionScorePrim()
csaSelectionScore
as a primitive int.
csaSelectionScore
public java.lang.Float getCsaSelectionScore()
csaSelectionScore
.
csaSelectionScore
public void setCsaSelectionScore(java.lang.Float csaSelectionScore)
csaSelectionScore
.
csaSelectionScore
- csaSelectionScore
public uk.ac.sanger.cgp.autocsa.interfaces.CsaTraceInterface getCsaTrace()
public void setCsaTrace(uk.ac.sanger.cgp.autocsa.interfaces.CsaTraceInterface csaTrace)
csaTrace
- a CsaTrace implementationpublic uk.ac.sanger.cgp.autocsa.beans.CSAOutput getCompResult()
public void setCompResult(uk.ac.sanger.cgp.autocsa.beans.CSAOutput compResult)
compResult
- a CSAOutput objectpublic boolean isCompared()
public java.lang.String getTraceStatus()
public void setTraceStatus(java.lang.String traceStatus)
traceStatus
- textual description of the experiment statuspublic boolean isBest()
csaSelectionScore
.
public void setBest(boolean best)
best
- true when best wildtype experimentpublic java.lang.String getComplimentFileName()
runNumber
for experiment pairing.
public ExperimentBean getComplimentExp()
runNumber
for experiment pairing.
public void setComplimentExp(ExperimentBean complimentExp)
runNumber
for experiment pairing.
complimentExp
- an ExperimentBean of any compliment experimentpublic boolean isComplimentPresent()
runNumber
for experiment pairing.
public uk.ac.sanger.cgp.autocsa.beans.Mutation getVariantToRender()
public java.util.Map getVariantGroups()
public void setVariantToRender(uk.ac.sanger.cgp.autocsa.beans.Mutation variantToRender)
variantToRender
- variant to renderpublic boolean isSubsPresent()
public void setSubsPresent(boolean subsPresent)
subsPresent
- true when substitution variants are availablepublic boolean isOthersPresent()
public void setOthersPresent(boolean othersPresent)
othersPresent
- true when non-substitution variants are availablepublic int getStrandPreFlaggingCountStatus()
Constants.PreFlagging
Constants.PreFlagging
public void setStrandPreFlaggingCountStatus(int strandPreFlaggingCountStatus)
Constants.PreFlagging
strandPreFlaggingCountStatus
- constant controlled status, see Constants.PreFlagging
public boolean isFlagAssessed()
public void setFlagAssessed(boolean flagAssessed)
flagAssessed
- true when flagging has been attempted on this experimentpublic java.lang.String toString()
toString
in class java.lang.Object
public int compareTo(java.lang.Object o)
compareTo
in interface java.lang.Comparable
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
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