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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
public class FileProcessingInfoBean
Object to hold all information related to file name construction and processing loaded from standaloneCsa.properties.
All values initialised to invalid values.
Constructor Summary | |
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FileProcessingInfoBean()
Creates a new empty instance of FileProcessingInfoBean. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public FileProcessingInfoBean()
Method Detail |
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public int getAmplimerPos()
public void setAmplimerPos(int aAmplimerPos)
aAmplimerPos
- position in the file name that represents the amplimer namepublic int getDnaNamePos()
public void setDnaNamePos(int aDnaNamePos)
aDnaNamePos
- position in the file name that represents the DNA/sample namepublic int getSampleTypePos()
public void setSampleTypePos(int aSampleTypePos)
aSampleTypePos
- position in the file name that represents the type of samplepublic int getDirectionPos()
public void setDirectionPos(int aDirectionPos)
aDirectionPos
- position in the file name that represents the direction of sequencingpublic int getRunPos()
public void setRunPos(int aRunPos)
aRunPos
- position in the file name that represents the run numberpublic char getDelimiter()
public void setDelimiter(char delimiter)
delimiter
- the char used to divide the filenamepublic java.lang.String getWildtypeIdentifier()
public void setWildtypeIdentifier(java.lang.String wildtypeIdentifier)
wildtypeIdentifier
- text indicating a wildtype sample/DNApublic java.lang.String getFileExtension()
public void setFileExtension(java.lang.String fileExtension)
fileExtension
- the file extension for the input sequencing filespublic char getSenseIdentifier()
public void setSenseIdentifier(char senseIdentifier)
senseIdentifier
- the character indicating a sense/forward sequencing filepublic char getAntisenseIdentifier()
public void setAntisenseIdentifier(char antisenseIdentifier)
antisenseIdentifier
- the character indicating an antisense/reverse sequencing filepublic boolean mobilityCorrectionRequired()
public void setMobilityCorrect(boolean mobilityCorrect)
mobilityCorrect
- true when mobility correction should be performed (and 'scf')public java.lang.String toString()
toString
in class java.lang.Object
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