java.lang.Object
- ubic.gemma.core.analysis.preprocess.filter.FilterConfig

All Implemented Interfaces:

Serializable
```
public class FilterConfig
extends Object
implements Serializable
```
Holds settings for filtering.

Author:

Paul

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`static double`	`DEFAULT_DISTINCTVALUE_FRACTION`
`static double`	`DEFAULT_HIGHEXPRESSION_CUT`
`static double`	`DEFAULT_LOWEXPRESSIONCUT`
`static double`	`DEFAULT_LOWVARIANCECUT`
`static double`	`DEFAULT_MINPRESENT_FRACTION`
`static double`	`DEFAULT_TOOSMALLTOKEEP`
`static int`	`MINIMUM_ROWS_TO_BOTHER`	Fewer rows than this, and we bail.
`static int`	`MINIMUM_SAMPLE`	How many samples a dataset has to have before we consider analyzing it.

Constructor Summary

Constructors
Constructor Description

FilterConfig()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getAfterDistinctValueCut()`
`int`	`getAfterInitialFilter()`
`int`	`getAfterLowExpressionCut()`
`int`	`getAfterLowVarianceCut()`
`int`	`getAfterMinPresentFilter()`
`int`	`getAfterZeroVarianceCut()`
`double`	`getHighExpressionCut()`
`double`	`getLowDistinctValueCut()`
`double`	`getLowExpressionCut()`
`double`	`getLowVarianceCut()`
`double`	`getMinPresentFraction()`
`int`	`getStartingRows()`
`boolean`	`isIgnoreMinimumRowsThreshold()`
`boolean`	`isIgnoreMinimumSampleThreshold()`
`boolean`	`isLogTransform()`
`boolean`	`isLowDistinctValueIsSet()`
`boolean`	`isLowExpressionCutIsSet()`
`boolean`	`isLowVarianceCutIsSet()`
`boolean`	`isMinPresentFractionIsSet()`
`boolean`	`isRequireSequences()`
`void`	`setAfterDistinctValueCut(int afterDistinctValueCut)`
`void`	`setAfterInitialFilter(int afterInitialFilter)`
`void`	`setAfterLowExpressionCut(int afterLowExpressionCut)`
`void`	`setAfterLowVarianceCut(int afterLowVarianceCut)`
`void`	`setAfterMinPresentFilter(int afterMinPresentFilter)`
`void`	`setAfterZeroVarianceCut(int afterZeroVarianceCut)`
`void`	`setHighExpressionCut(double highExpressionCut)`
`void`	`setIgnoreMinimumRowsThreshold(boolean ignoreMinimumRowsThreshold)`
`void`	`setIgnoreMinimumSampleThreshold(boolean ignoreMinimumSampleThreshold)`
`void`	`setLogTransform(boolean logTransform)`
`void`	`setLowDistinctValueCut(double lowDistinctValueCut)`
`void`	`setLowExpressionCut(double lowExpressionCut)`
`void`	`setLowVarianceCut(double lowVarianceCut)`
`void`	`setMinPresentFraction(double minPresentFraction)`
`void`	`setRequireSequences(boolean requireSequences)`	Set to true if rows lacking associated BioSequences for the element should be removed.
`void`	`setStartingRows(int startingRows)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail
- DEFAULT_DISTINCTVALUE_FRACTION
```
public static final double DEFAULT_DISTINCTVALUE_FRACTION
```
  See Also:
  
  Constant Field Values
- DEFAULT_HIGHEXPRESSION_CUT
```
public static final double DEFAULT_HIGHEXPRESSION_CUT
```
  See Also:
  
  Constant Field Values
- DEFAULT_LOWEXPRESSIONCUT
```
public static final double DEFAULT_LOWEXPRESSIONCUT
```
  See Also:
  
  Constant Field Values
- DEFAULT_LOWVARIANCECUT
```
public static final double DEFAULT_LOWVARIANCECUT
```
  See Also:
  
  Constant Field Values
- DEFAULT_MINPRESENT_FRACTION
```
public static final double DEFAULT_MINPRESENT_FRACTION
```
  See Also:
  
  Constant Field Values
- DEFAULT_TOOSMALLTOKEEP
```
public static final double DEFAULT_TOOSMALLTOKEEP
```
  See Also:
  
  Constant Field Values
- MINIMUM_ROWS_TO_BOTHER
```
public static final int MINIMUM_ROWS_TO_BOTHER
```
  Fewer rows than this, and we bail.
  
  See Also:
  
  Constant Field Values
- MINIMUM_SAMPLE
```
public static final int MINIMUM_SAMPLE
```
  How many samples a dataset has to have before we consider analyzing it.
  
  See Also:
  
  for a related setting., Constant Field Values

Constructor Detail
- FilterConfig
```
public FilterConfig()
```

Method Detail

isRequireSequences
```
public boolean isRequireSequences()
```

setRequireSequences
```
public void setRequireSequences(boolean requireSequences)
```
Set to true if rows lacking associated BioSequences for the element should be removed.

Parameters:

requireSequences - new value

isLowDistinctValueIsSet

public boolean isLowDistinctValueIsSet()

getAfterDistinctValueCut
```
public int getAfterDistinctValueCut()
```

setAfterDistinctValueCut

public void setAfterDistinctValueCut(int afterDistinctValueCut)

getAfterInitialFilter
```
public int getAfterInitialFilter()
```
Returns:

the afterInitialFilter

setAfterInitialFilter
```
public void setAfterInitialFilter(int afterInitialFilter)
```
Parameters:

afterInitialFilter - the afterInitialFilter to set

getAfterLowExpressionCut
```
public int getAfterLowExpressionCut()
```
Returns:

the afterLowExpressionCut

setAfterLowExpressionCut
```
public void setAfterLowExpressionCut(int afterLowExpressionCut)
```
Parameters:

afterLowExpressionCut - the afterLowExpressionCut to set

getAfterLowVarianceCut
```
public int getAfterLowVarianceCut()
```
Returns:

the afterLowVarianceCut

setAfterLowVarianceCut
```
public void setAfterLowVarianceCut(int afterLowVarianceCut)
```
Parameters:

afterLowVarianceCut - the afterLowVarianceCut to set

getAfterMinPresentFilter
```
public int getAfterMinPresentFilter()
```
Returns:

the afterMinPresentFilter

setAfterMinPresentFilter
```
public void setAfterMinPresentFilter(int afterMinPresentFilter)
```
Parameters:

afterMinPresentFilter - the afterMinPresentFilter to set

getAfterZeroVarianceCut
```
public int getAfterZeroVarianceCut()
```

setAfterZeroVarianceCut

public void setAfterZeroVarianceCut(int afterZeroVarianceCut)

getHighExpressionCut
```
public double getHighExpressionCut()
```

setHighExpressionCut

public void setHighExpressionCut(double highExpressionCut)

getLowDistinctValueCut

public double getLowDistinctValueCut()

setLowDistinctValueCut

public void setLowDistinctValueCut(double lowDistinctValueCut)

getLowExpressionCut
```
public double getLowExpressionCut()
```

setLowExpressionCut

public void setLowExpressionCut(double lowExpressionCut)

getLowVarianceCut
```
public double getLowVarianceCut()
```

setLowVarianceCut

public void setLowVarianceCut(double lowVarianceCut)

getMinPresentFraction
```
public double getMinPresentFraction()
```

setMinPresentFraction

public void setMinPresentFraction(double minPresentFraction)

getStartingRows
```
public int getStartingRows()
```
Returns:

the startingRows

setStartingRows
```
public void setStartingRows(int startingRows)
```
Parameters:

startingRows - the startingRows to set

isIgnoreMinimumRowsThreshold
```
public boolean isIgnoreMinimumRowsThreshold()
```
Returns:

the ignoreMinimumRowThreshold

setIgnoreMinimumRowsThreshold
```
public void setIgnoreMinimumRowsThreshold(boolean ignoreMinimumRowsThreshold)
```
Parameters:

ignoreMinimumRowsThreshold - the ignoreMinimumRowThreshold to set

isIgnoreMinimumSampleThreshold

public boolean isIgnoreMinimumSampleThreshold()

setIgnoreMinimumSampleThreshold

public void setIgnoreMinimumSampleThreshold(boolean ignoreMinimumSampleThreshold)

isLogTransform
```
public boolean isLogTransform()
```
Returns:

the logTransform

setLogTransform
```
public void setLogTransform(boolean logTransform)
```
Parameters:

logTransform - the logTransform to set

isLowExpressionCutIsSet

public boolean isLowExpressionCutIsSet()

isLowVarianceCutIsSet

public boolean isLowVarianceCutIsSet()

isMinPresentFractionIsSet

public boolean isMinPresentFractionIsSet()

toString
```
public String toString()
```
Overrides:

toString in class Object

Class FilterConfig

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_DISTINCTVALUE_FRACTION

DEFAULT_HIGHEXPRESSION_CUT

DEFAULT_LOWEXPRESSIONCUT

DEFAULT_LOWVARIANCECUT

DEFAULT_MINPRESENT_FRACTION

DEFAULT_TOOSMALLTOKEEP

MINIMUM_ROWS_TO_BOTHER

MINIMUM_SAMPLE

Constructor Detail

FilterConfig

Method Detail

isRequireSequences

setRequireSequences

isLowDistinctValueIsSet

getAfterDistinctValueCut

setAfterDistinctValueCut

getAfterInitialFilter

setAfterInitialFilter

getAfterLowExpressionCut

setAfterLowExpressionCut

getAfterLowVarianceCut

setAfterLowVarianceCut

getAfterMinPresentFilter

setAfterMinPresentFilter

getAfterZeroVarianceCut

setAfterZeroVarianceCut

getHighExpressionCut

setHighExpressionCut

getLowDistinctValueCut

setLowDistinctValueCut

getLowExpressionCut

setLowExpressionCut

getLowVarianceCut

setLowVarianceCut

getMinPresentFraction

setMinPresentFraction

getStartingRows

setStartingRows

isIgnoreMinimumRowsThreshold

setIgnoreMinimumRowsThreshold

isIgnoreMinimumSampleThreshold

setIgnoreMinimumSampleThreshold

isLogTransform

setLogTransform

isLowExpressionCutIsSet

isLowVarianceCutIsSet

isMinPresentFractionIsSet

toString