edu.mayo.bsi.ngsportal.shared
Class SampleInfo

java.lang.Object
  edu.mayo.bsi.ngsportal.shared.SampleInfo

All Implemented Interfaces:

com.google.gwt.user.client.rpc.IsSerializable

public class SampleInfo
extends Object
implements com.google.gwt.user.client.rpc.IsSerializable

@author Gregory Dougherty

Constructor Summary

SampleInfo(int id, int sampleID, String name, String runName, String appType, String readType, int lane, int cycles, boolean isControl, boolean isIndexVendor, String indexSeq, String flowCell, String rlimsID, String sampleRLIMSID, String parentID, String captureKit, String rlimsProject, String species, String diseaseType, String[] fileLocation, long fileSize, String keepRequestor, Date keepDate, String dataFileName, boolean isCim, Boolean isBic)
Normal Constructor

SampleInfo(int id, String sampleRLIMSID, String parentID, String species, String diseaseType)
No Sequenced Sample Info Constructor

Method Summary

void	addNonPI(String nonPIName) Add a non-PI to the list of non-PIs for this sample
void	addPI(String piName) Add a PI to the list of PIs for this sample
boolean	equals(Object obj)
String	getAppType()
String	getCaptureKit()
int	getCycles()
String	getDataFileName()
String	getDiseaseType()
String[]	getFileLocation()
String	getFileLocationAsString() Take the array of 0 or more file locations, and turn it into a string
long	getFileSize()
String	getFlowCell()
static SampleInfo	getFromListByID(List<SampleInfo> theList, int theID) Determines if theList contains a Sample that has the sampleID theID
static SampleInfo	getFromListBySampleID(List<SampleInfo> theList, int theID) Determines if theList contains a Sample that has the sampleID theID
int	getID()
String	getIndexSeq()
Date	getKeepDate()
String	getKeepRequestor()
int	getLane()
String	getName()
List<String>	getNonPIs()
String	getParentID()
List<String>	getPIs()
List<QCResult>	getQCResult()
String	getReadType()
String	getRlimsID()
String	getRLIMSProject()
String	getRunName()
int	getSampleID()
String	getSampleRlimsID()
String	getSampleString() Get a String that uniquely identifies a Sample (w/o any Sequenced Sample information)
String	getSpecies()
int	hashCode()
Boolean	isBic()
boolean	isCim()
boolean	isControl()
boolean	isIndexVendor()
boolean	isInList(List<SampleInfo> theList) Determines if theList contains a Sample that has the same sampleID as this Sample
boolean	isQCPopulated()
static String	makePI(String firstName, String lastName) Make a string representing a PI or non-PI
boolean	needsUpdate(String theSpecies, String theDiseaseType) Checks to see if any of the passed in values are meaningful and different from the existing values
boolean	needsUpdate(String theName, String theAppType, String theReadType, int theLane, int theCycles, String theRlimsID, String theCaptureKit, String theRLIMSProject, boolean newControl, boolean isVendor, String indexSequence, String theFlowCell, String theRunName, boolean isCIM, Boolean isBIC) Checks to see if any of the passed in values are meaningful and different from the existing values
static StringPair	parsePI(String piName) Parse a string representing a PI or non-PI, and turn it into a first name and last name
boolean	removeNonPI(String piName) Remove a non-PI from the list of non-PIs for this sample
boolean	removePI(String piName) Remove a PI from the list of PIs for this sample
boolean	seqNeedsUpdate(String theCaptureKit, String theRLIMSProjectID) Checks to see if any of the passed in values are meaningful and different from the existing values
void	setID(int id)
void	setName(String name)
void	setParentID(String parentID)
void	setQCPopulated(boolean isQCPopulated)
void	setQCResult(List<QCResult> qcResult) Update the QC Result List.
void	setSampleID(int sampleID)
void	setSampleRlimsID(String sampleRLIMSID)
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SampleInfo

public SampleInfo(int id,
                  int sampleID,
                  String name,
                  String runName,
                  String appType,
                  String readType,
                  int lane,
                  int cycles,
                  boolean isControl,
                  boolean isIndexVendor,
                  String indexSeq,
                  String flowCell,
                  String rlimsID,
                  String sampleRLIMSID,
                  String parentID,
                  String captureKit,
                  String rlimsProject,
                  String species,
                  String diseaseType,
                  String[] fileLocation,
                  long fileSize,
                  String keepRequestor,
                  Date keepDate,
                  String dataFileName,
                  boolean isCim,
                  Boolean isBic)

Normal Constructor

Parameters:

id - DB Row ID of the Sequenced Sample

sampleID - DB Row ID of the Sample

name - Name of the Sample

runName - Name of the Run

appType - Sequenced Sample application type

readType - Sequenced Sample read type

lane - Sequenced Sample lane

cycles - Sequenced Sample cycles

isControl - Was the Sequenced Sample a control

isIndexVendor - Was the Sequenced Sample's index from the Vendor

indexSeq - Sequenced Sample index, could be empty

flowCell - Sequenced Sample flow cell

rlimsID - Sequenced Sample RLIMS ID

sampleRLIMSID - Sample RLIMS Family ID, must never be empty or null

parentID - Sample RLIMS Parent ID, must never be empty or null

captureKit - The capture kit used to get the data

rlimsProject - The RLIMS Project the sample was sequenced as part of

species - Sample Species

diseaseType - Disease type of the sample, if any

fileLocation - Locations where associated data files are stored, if any

fileSize - Size of the Primary analysis data file, or 0 if none

keepRequestor - Person who requested the data files be kept, or null if no such request

keepDate - Date to keep Primary analysis files until, or null of not keeping files

dataFileName - Name of the data file that overrides the default data file name

isCim - True if sample was sequenced for CIM, false otherwise

isBic - True if was sequenced for BIC, false if not, NULL if not known

SampleInfo

public SampleInfo(int id,
                  String sampleRLIMSID,
                  String parentID,
                  String species,
                  String diseaseType)

No Sequenced Sample Info Constructor

Parameters:

id - DB Row ID of the Sample

sampleRLIMSID - Sample RLIMS Family ID, must never be empty or null

parentID - Sample RLIMS Parent ID, must never be empty or null

species - Sample Species

diseaseType - Disease type of the sample, if any

Method Detail

getFromListBySampleID

public static final SampleInfo getFromListBySampleID(List<SampleInfo> theList,
                                                     int theID)

Determines if theList contains a Sample that has the sampleID theID

Parameters:

theList - List to check. Will return null if list is null or empty

theID - Sample ID we're looking for

Returns:

The first matching sample if theList is not null, and has a matching sample in it, else null

getFromListByID

public static final SampleInfo getFromListByID(List<SampleInfo> theList,
                                               int theID)

Determines if theList contains a Sample that has the sampleID theID

Parameters:

theList - List to check. Will return null if list is null or empty

theID - ID we're looking for

Returns:

The first matching sample if theList is not null, and has a matching sample in it, else null

makePI

public static final String makePI(String firstName,
                                  String lastName)

Make a string representing a PI or non-PI

Parameters:

firstName - The person's first name. Will use "null" if null, "" if empty

lastName - The person's last name. Will use "null" if null, "" if empty

Returns:

String representing the person

parsePI

public static final StringPair parsePI(String piName)

Parse a string representing a PI or non-PI, and turn it into a first name and last name

Parameters:

piName - The person's last name. Will use "null" if null, "" if empty

Returns:

StringPair representing the person, never null, and neither name will be null

isInList

public boolean isInList(List<SampleInfo> theList)

Determines if theList contains a Sample that has the same sampleID as this Sample

Parameters:

theList - List to check. Will return false if list is null or empty

Returns:

True if theList is not null, and has a matching sample in it

needsUpdate

public boolean needsUpdate(String theSpecies,
                           String theDiseaseType)

Checks to see if any of the passed in values are meaningful and different from the existing values

Parameters:

theSpecies - The species of the sample

theDiseaseType - The diseaseType of the sample, or null if have nothing

Returns:

True if a passed in value was different, and the sample needs to be re-saved to the DB, else false

seqNeedsUpdate

public boolean seqNeedsUpdate(String theCaptureKit,
                              String theRLIMSProjectID)

Checks to see if any of the passed in values are meaningful and different from the existing values

Parameters:

theCaptureKit - The capture kit of the sample

theRLIMSProjectID - The RLIMS Project ID of the sample

Returns:

True if a passed in value was different, and the sample needs to be re-saved to the DB, else false

needsUpdate

public boolean needsUpdate(String theName,
                           String theAppType,
                           String theReadType,
                           int theLane,
                           int theCycles,
                           String theRlimsID,
                           String theCaptureKit,
                           String theRLIMSProject,
                           boolean newControl,
                           boolean isVendor,
                           String indexSequence,
                           String theFlowCell,
                           String theRunName,
                           boolean isCIM,
                           Boolean isBIC)

Checks to see if any of the passed in values are meaningful and different from the existing values

Parameters:

theName - The name of the sample

theAppType - The name of the type of sample

theReadType - The name of the read type

theLane - The lane number

theCycles - The number of cycles

theRlimsID - The value of the RLIMS ID

theCaptureKit - The Capture Kit used

theRLIMSProject - The RLIMS Project the sample was sequenced for

newControl - Whether the sample is a control

isVendor - Whether the sampleID is vendor supplied (only relevant if indexSequence is NOT null)

indexSequence - The sequence fragment tested (null if not an indexed sample)

theFlowCell - The flowCell the sequencing was done in

theRunName - The name of the run the sample belongs to

isCIM - True if was sequenced for CIM, false if not

isBIC - True if was sequenced for BIC, false if not, NULL if don't know

Returns:

True if a passed in value was different, and the sample needs to be re-saved to the DB, else false

getID

public final int getID()

Returns:

the id

setID

public final void setID(int id)

Parameters:

id - the id to set

getSampleID

public final int getSampleID()

Returns:

the sampleID

setSampleID

public final void setSampleID(int sampleID)

Parameters:

sampleID - the sampleID to set

getPIs

public final List<String> getPIs()

Returns:

the PIs. May be empty list, won't be null

addPI

public final void addPI(String piName)

Add a PI to the list of PIs for this sample

Parameters:

piName - The name of the PI, usually [Last], [First]

removePI

public final boolean removePI(String piName)

Remove a PI from the list of PIs for this sample

Parameters:

piName - The name of the PI, usually [Last], [First]

Returns:

True if had that PI, false if didn't

getNonPIs

public final List<String> getNonPIs()

Returns:

the non-PIs. May be empty list, won't be null

addNonPI

public final void addNonPI(String nonPIName)

Add a non-PI to the list of non-PIs for this sample

Parameters:

nonPIName - The name of the non-PI, usually [Last], [First]

removeNonPI

public final boolean removeNonPI(String piName)

Remove a non-PI from the list of non-PIs for this sample

Parameters:

piName - The name of the non-PI, usually [Last], [First]

Returns:

True if had that non-PI, false if didn't

getName

public final String getName()

Returns:

the name

setName

public final void setName(String name)

Parameters:

name - the name to set

getRunName

public final String getRunName()

Returns:

the runName

getAppType

public final String getAppType()

Returns:

the appType

getReadType

public final String getReadType()

Returns:

the readType

getLane

public final int getLane()

Returns:

the lane

getCycles

public final int getCycles()

Returns:

the cycles

isControl

public final boolean isControl()

Returns:

the isControl

isCim

public boolean isCim()

Returns:

True if sequenced for CIM, false otherwise

isBic

public Boolean isBic()

Returns:

True if sequenced for BIC, false if not, NULL if unknown

isIndexVendor

public final boolean isIndexVendor()

Returns:

the isIndexVendor

getIndexSeq

public final String getIndexSeq()

Returns:

the indexSeq

getFlowCell

public final String getFlowCell()

Returns:

the flowCell

getDataFileName

public final String getDataFileName()

Returns:

the dataFileName

getRlimsID

public final String getRlimsID()

Returns:

the rlimsID

getSampleRlimsID

public final String getSampleRlimsID()

Returns:

the sampleRLIMSID, Should never be empty or null

setSampleRlimsID

public final void setSampleRlimsID(String sampleRLIMSID)

Parameters:

sampleRLIMSID - the sampleRLIMSID to set

getParentID

public String getParentID()

Returns:

the parentID, Should never be empty or null

setParentID

public final void setParentID(String parentID)

Parameters:

parentID - the parentID to set

getCaptureKit

public final String getCaptureKit()

Returns:

the captureKit

getRLIMSProject

public final String getRLIMSProject()

Returns:

the rlimsProject

getSpecies

public final String getSpecies()

Returns:

the species

getDiseaseType

public final String getDiseaseType()

Returns:

the diseaseType

getFileLocation

public final String[] getFileLocation()

Returns:

the fileLocation

getFileLocationAsString

public final String getFileLocationAsString()

Take the array of 0 or more file locations, and turn it into a string

Returns:

A string. if no file locations, will be empty. If one file location, will be that file location. If more than one file location, will be returned as quoted strings separated by commas

getFileSize

public final long getFileSize()

Returns:

the fileSize

getKeepRequestor

public final String getKeepRequestor()

Returns:

the keepRequestor

getKeepDate

public final Date getKeepDate()

Returns:

the keepDate

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

getSampleString

public String getSampleString()

Get a String that uniquely identifies a Sample (w/o any Sequenced Sample information)

Returns:

A String that uniquely identifies this sample: "[name] : [species] : [Sample RLIMS ID] : [Disease Type] : [PIs]"

getQCResult

public List<QCResult> getQCResult()

Returns:

List of QC Results

setQCResult

public void setQCResult(List<QCResult> qcResult)

Update the QC Result List. No error checking is done on the passed in data

Parameters:

qcResult - New List to use

isQCPopulated

public boolean isQCPopulated()

Returns:

True if isQCPopulated

setQCPopulated

public void setQCPopulated(boolean isQCPopulated)

Parameters:

isQCPopulated - New value for isQCPopulated