edu.mayo.bsi.ngsportal.server
Class SampleData

java.lang.Object
  edu.mayo.bsi.ngsportal.server.SampleData

public class SampleData
extends Object

Class holding the sample data from a Sequenced Sample, so it can be printed out

@author Gregory Dougherty

Constructor Summary

SampleData(ContactInfo thePI, RunData theRun, String sampleName, String appType, String readType, int lane, int cycles, int numReads, boolean isControl, boolean isIndexVendor, String indexSeq, String rlimsProjectID, String sampleFamilyID, String sampleParentID, String sampleRLIMSID)
Constructor for PI and numReads

SampleData(RunData theRun, String sampleName, String appType, String readType, int lane, int cycles, boolean isControl, boolean isIndexVendor, String indexSeq, String rlimsProjectID, String sampleFamilyID, String sampleParentID, String sampleRLIMSID)
Normal Constructor

Method Summary

int	getNumReads() Get the number of reads
String	getRunName() Return the run name, or an empty string if it doesn't have one
ContactInfo	getThePI() Get ContactInfo information about the PI
static String	toTabHeader() Get a header describing the data as a Tab delimited string
String	toTabString() Get the SampleData as a tab delimited string, in the order specified by ()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SampleData

public SampleData(RunData theRun,
                  String sampleName,
                  String appType,
                  String readType,
                  int lane,
                  int cycles,
                  boolean isControl,
                  boolean isIndexVendor,
                  String indexSeq,
                  String rlimsProjectID,
                  String sampleFamilyID,
                  String sampleParentID,
                  String sampleRLIMSID)

Normal Constructor

Parameters:

theRun - Run the Sample belongs to

sampleName - Sample name

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

rlimsProjectID - Sequenced Sample RLIMS Project ID

sampleFamilyID - Sample Family ID

sampleParentID - Sample Parent ID

sampleRLIMSID - Sequenced Sample RLIMS ID

SampleData

public SampleData(ContactInfo thePI,
                  RunData theRun,
                  String sampleName,
                  String appType,
                  String readType,
                  int lane,
                  int cycles,
                  int numReads,
                  boolean isControl,
                  boolean isIndexVendor,
                  String indexSeq,
                  String rlimsProjectID,
                  String sampleFamilyID,
                  String sampleParentID,
                  String sampleRLIMSID)

Constructor for PI and numReads

Parameters:

thePI - PI the Sample belongs to

theRun - Run the Sample belongs to

sampleName - Sample name

appType - Sequenced Sample application type

readType - Sequenced Sample read type

lane - Sequenced Sample lane

cycles - Sequenced Sample cycles

numReads - Flagstat number of reads

isControl - Was the Sequenced Sample a control

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

indexSeq - Sequenced Sample index, could be empty

rlimsProjectID - Sequenced Sample RLIMS Project ID

sampleFamilyID - Sample Family ID

sampleParentID - Sample Parent ID

sampleRLIMSID - Sequenced Sample RLIMS ID

Method Detail

getThePI

public final ContactInfo getThePI()

Get ContactInfo information about the PI

Returns:

the thePI

getNumReads

public final int getNumReads()

Get the number of reads

Returns:

the numReads

toTabHeader

public static String toTabHeader()

Get a header describing the data as a Tab delimited string

Returns:

Tab delimited string holding the header defining what comes from (). It starts with the output from (), and continues with:
Sample Name Sample RLIMS ID Sequencing RLIMS Project ID Lane App Type Read Type
Num Cycles Is Control Is Vendor Index Index Sequence

getRunName

public String getRunName()

Return the run name, or an empty string if it doesn't have one

Returns:

A string

toTabString

public String toTabString()

Get the SampleData as a tab delimited string, in the order specified by ()

Returns:

Tab delimited string with the contents of the sample and its run
It starts with the output from (), and continues with:
Sample Name Sample Family ID Sample Parent ID Sample RLIMS ID Sequencing RLIMS Project ID
Lane App Type Read Type Num Cycles Is Control Is Vendor Index Index Sequence