uk.ac.sanger.cgp.standalonecsa.beans
Class FileProcessingInfoBean

java.lang.Object
  extended by uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

public class FileProcessingInfoBean
extends java.lang.Object

Object to hold all information related to file name construction and processing loaded from standaloneCsa.properties.
All values initialised to invalid values.

Author:
Original: kr2, $Author: kr2 $

Constructor Summary
FileProcessingInfoBean()
          Creates a new empty instance of FileProcessingInfoBean.
 
Method Summary
 int getAmplimerPos()
          Get the position in the file name, once split on the delimiter, that represents the amplimer name.
 char getAntisenseIdentifier()
          Get the character indicating an antisense/reverse sequencing file.
 char getDelimiter()
          Get the character that has been used to divide filename components e.g.
 int getDirectionPos()
          Get the position in the file name, once split on the delimiter, that represents the sequencing direction.
 int getDnaNamePos()
          Get the position in the file name, once split on the delimiter, that represents the DNA/sample name.
 java.lang.String getFileExtension()
          Get the file extension for the input sequencing files.
 int getRunPos()
          Get the position in the file name, once split on the delimiter, that represents the run position.
 int getSampleTypePos()
          Get the position in the file name, once split on the delimiter, that represents the sample type.
 char getSenseIdentifier()
          Get the character indicating a sense/forward sequencing file.
 java.lang.String getWildtypeIdentifier()
          Get the text that indicates a wildtype sample/DNA.
 boolean mobilityCorrectionRequired()
          True when mobility correction should be performed, only affects 'scf' files and currently not a valid option.
 void setAmplimerPos(int aAmplimerPos)
          Set the position in the file name, once split on the delimiter, that represents the amplimer name.
 void setAntisenseIdentifier(char antisenseIdentifier)
          Set the character indicating an antisense/reverse sequencing file.
 void setDelimiter(char delimiter)
          Set the character that has been used to divide filename components e.g.
 void setDirectionPos(int aDirectionPos)
          Set the position in the file name, once split on the delimiter, that represents the direction of sequencing.
 void setDnaNamePos(int aDnaNamePos)
          Set the position in the file name, once split on the delimiter, that represents the DNA/sample name.
 void setFileExtension(java.lang.String fileExtension)
          Set the file extension for the input sequencing files.
 void setMobilityCorrect(boolean mobilityCorrect)
          Set to true if mobility correction should be performed, only affects 'scf' files and currently not a valid option.
 void setRunPos(int aRunPos)
          Set the position in the file name, once split on the delimiter, that represents the run number.
 void setSampleTypePos(int aSampleTypePos)
          Set the position in the file name, once split on the delimiter, that represents the type of sample.
 void setSenseIdentifier(char senseIdentifier)
          Set the character indicating a sense/forward sequencing file.
 void setWildtypeIdentifier(java.lang.String wildtypeIdentifier)
          Set the text that indicates a wildtype sample/DNA.
 java.lang.String toString()
          Get a string representation of this object.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

FileProcessingInfoBean

public FileProcessingInfoBean()
Creates a new empty instance of FileProcessingInfoBean.

Method Detail

getAmplimerPos

public int getAmplimerPos()
Get the position in the file name, once split on the delimiter, that represents the amplimer name.

Returns:
an integer position in the split filename

setAmplimerPos

public void setAmplimerPos(int aAmplimerPos)
Set the position in the file name, once split on the delimiter, that represents the amplimer name.

Parameters:
aAmplimerPos - position in the file name that represents the amplimer name

getDnaNamePos

public int getDnaNamePos()
Get the position in the file name, once split on the delimiter, that represents the DNA/sample name.

Returns:
an integer position in the split filename

setDnaNamePos

public void setDnaNamePos(int aDnaNamePos)
Set the position in the file name, once split on the delimiter, that represents the DNA/sample name.

Parameters:
aDnaNamePos - position in the file name that represents the DNA/sample name

getSampleTypePos

public int getSampleTypePos()
Get the position in the file name, once split on the delimiter, that represents the sample type.

Returns:
an integer position in the split filename

setSampleTypePos

public void setSampleTypePos(int aSampleTypePos)
Set the position in the file name, once split on the delimiter, that represents the type of sample.

Parameters:
aSampleTypePos - position in the file name that represents the type of sample

getDirectionPos

public int getDirectionPos()
Get the position in the file name, once split on the delimiter, that represents the sequencing direction.

Returns:
an integer position in the split filename

setDirectionPos

public void setDirectionPos(int aDirectionPos)
Set the position in the file name, once split on the delimiter, that represents the direction of sequencing.

Parameters:
aDirectionPos - position in the file name that represents the direction of sequencing

getRunPos

public int getRunPos()
Get the position in the file name, once split on the delimiter, that represents the run position.

Returns:
an integer position in the split filename

setRunPos

public void setRunPos(int aRunPos)
Set the position in the file name, once split on the delimiter, that represents the run number.

Parameters:
aRunPos - position in the file name that represents the run number

getDelimiter

public char getDelimiter()
Get the character that has been used to divide filename components e.g. '_'

Returns:
the char used to divide the filename

setDelimiter

public void setDelimiter(char delimiter)
Set the character that has been used to divide filename components e.g. '_'

Parameters:
delimiter - the char used to divide the filename

getWildtypeIdentifier

public java.lang.String getWildtypeIdentifier()
Get the text that indicates a wildtype sample/DNA.

Returns:
text indicating a wildtype sample/DNA

setWildtypeIdentifier

public void setWildtypeIdentifier(java.lang.String wildtypeIdentifier)
Set the text that indicates a wildtype sample/DNA.

Parameters:
wildtypeIdentifier - text indicating a wildtype sample/DNA

getFileExtension

public java.lang.String getFileExtension()
Get the file extension for the input sequencing files. 'ab1' and 'scf' are currently valid.

Returns:
the file extension for the input sequencing files

setFileExtension

public void setFileExtension(java.lang.String fileExtension)
Set the file extension for the input sequencing files. 'ab1' and 'scf' are currently valid.

Parameters:
fileExtension - the file extension for the input sequencing files

getSenseIdentifier

public char getSenseIdentifier()
Get the character indicating a sense/forward sequencing file.

Returns:
the character indicating a sense/forward sequencing file

setSenseIdentifier

public void setSenseIdentifier(char senseIdentifier)
Set the character indicating a sense/forward sequencing file.

Parameters:
senseIdentifier - the character indicating a sense/forward sequencing file

getAntisenseIdentifier

public char getAntisenseIdentifier()
Get the character indicating an antisense/reverse sequencing file.

Returns:
the character indicating an antisense/reverse sequencing file

setAntisenseIdentifier

public void setAntisenseIdentifier(char antisenseIdentifier)
Set the character indicating an antisense/reverse sequencing file.

Parameters:
antisenseIdentifier - the character indicating an antisense/reverse sequencing file

mobilityCorrectionRequired

public boolean mobilityCorrectionRequired()
True when mobility correction should be performed, only affects 'scf' files and currently not a valid option.

Returns:
true when mobility correction should be performed (and 'scf')

setMobilityCorrect

public void setMobilityCorrect(boolean mobilityCorrect)
Set to true if mobility correction should be performed, only affects 'scf' files and currently not a valid option.

Parameters:
mobilityCorrect - true when mobility correction should be performed (and 'scf')

toString

public java.lang.String toString()
Get a string representation of this object.

Overrides:
toString in class java.lang.Object
Returns:
string representation of this object