apollo.analysis
Class RemoteBlastNCBI.BlastOptions

java.lang.Object
  apollo.analysis.RemoteBlastNCBI.BlastOptions

Enclosing class:

RemoteBlastNCBI

public static class RemoteBlastNCBI.BlastOptions
extends java.lang.Object

Options for running qBLAST.

Constructor Summary

RemoteBlastNCBI.BlastOptions()
Constructor.

Method Summary

int	getGapExtendCost() Get the cost of extending a gap in an alignment.
int	getGapOpenCost() Get the cost of opening a gap in an alignment.
int	getGeneticCode() Get the organism's genetic code.
int	getNumberOfHits() Get the maximum number of hits to calculate.
boolean	isSetFilterHumanRepeats() Checks whether human repeat filtering is enabled.
boolean	isSetFilterLowComplexity() Checks whether low complexity filtering is enabled.
boolean	isSetFilterMaskLookup() Checks whether masked sequence filtering is enabled.
void	setFilterHumanRepeats(boolean humanRepeatFiltering) Set human repeat filtering.
void	setFilterLowComplexity(boolean lowComplexityFiltering) Set low complexity filtering.
void	setFilterMaskLookup(boolean maskFilter) Set masked sequence filtering.
void	setGapExtendCost(int gapExtendCost) Set the cost of extending a gap in an alignment.
void	setGapOpenCost(int gapOpenCost) Set the cost of opening a gap in an alignment.
void	setGeneticCode(int geneticCode) Set the organism's genetic code.
void	setNumberOfHits(int numberOfHits) Set the maximum number of hits to calculate.

Methods inherited from class java.lang.Object

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

Constructor Detail

RemoteBlastNCBI.BlastOptions

public RemoteBlastNCBI.BlastOptions()

Constructor.

Method Detail

getGeneticCode

public int getGeneticCode()

Get the organism's genetic code.

Returns:

organism's genetic code

setGeneticCode

public void setGeneticCode(int geneticCode)

Set the organism's genetic code.

Parameters:

geneticCode - - organism's genetic code

isSetFilterLowComplexity

public boolean isSetFilterLowComplexity()

Checks whether low complexity filtering is enabled.

Returns:

true if low complexity filtering is enabled

setFilterLowComplexity

public void setFilterLowComplexity(boolean lowComplexityFiltering)

Set low complexity filtering.

Parameters:

lowComplexityFiltering - - whether to enable low complexity filtering

isSetFilterHumanRepeats

public boolean isSetFilterHumanRepeats()

Checks whether human repeat filtering is enabled.

Returns:

true if human repeat filtering is enabled

setFilterHumanRepeats

public void setFilterHumanRepeats(boolean humanRepeatFiltering)

Set human repeat filtering.

Parameters:

humanRepeatFiltering - - whether to enable human repeat filtering

isSetFilterMaskLookup

public boolean isSetFilterMaskLookup()

Checks whether masked sequence filtering is enabled.

Returns:

true if masked sequence filtering is enabled

setFilterMaskLookup

public void setFilterMaskLookup(boolean maskFilter)

Set masked sequence filtering.

Parameters:

maskFilter - - whether to enable masked sequence filtering

getGapOpenCost

public int getGapOpenCost()

Get the cost of opening a gap in an alignment.

Returns:

cost of opening a gap

setGapOpenCost

public void setGapOpenCost(int gapOpenCost)

Set the cost of opening a gap in an alignment.

Parameters:

gapOpenCost - - cost of opening a gap

getGapExtendCost

public int getGapExtendCost()

Get the cost of extending a gap in an alignment.

Returns:

cost of extending a gap

setGapExtendCost

public void setGapExtendCost(int gapExtendCost)

Set the cost of extending a gap in an alignment.

Parameters:

gapExtendCost - - cost of extending a gap

getNumberOfHits

public int getNumberOfHits()

Get the maximum number of hits to calculate.

Returns:

- maximum number of hits to calculate

setNumberOfHits

public void setNumberOfHits(int numberOfHits)

Set the maximum number of hits to calculate.

Parameters:

numberOfHits - - maximum number of hits to calculate