org.geworkbench.bison.model.analysis
Class FilteringAnalysis

java.lang.Object
  extended by org.geworkbench.analysis.AbstractAnalysis
      extended by org.geworkbench.bison.model.analysis.FilteringAnalysis
All Implemented Interfaces:
java.io.Serializable, java.util.Observer, DSDescribable, Analysis

public abstract class FilteringAnalysis
extends AbstractAnalysis

Abstract class to tag filtering analysis and defines common methods for filtering.

Version:
$Id: FilteringAnalysis.java 8518 2011-11-09 16:45:58Z zji $
Author:
zji
See Also:
Serialized Form

Nested Class Summary
protected static class FilteringAnalysis.CriterionOption
           
 
Field Summary
protected  FilteringAnalysis.CriterionOption criterionOption
           
protected  java.lang.String expectedTypeName
           
protected  DSMicroarraySet maSet
           
protected  int numberThreshold
           
protected  double percentThreshold
           
 
Fields inherited from class org.geworkbench.analysis.AbstractAnalysis
AFFY_DETECTION_CALL_FILTER, ALLELIC_FREQUENCY_TYPE, aspp, BLAST_TYPE, DEVIATION_BASED_FILTER_TYPE, EXPRESSION_THRESHOLD_FILTER_TYPE, FOLD_CHANGE_TYPE, GENEPIX_FlAGS_FILTER_TYPE, HIERARCHICAL_CLUSTERING_TYPE, HOUSEKEEPINGGENES_VALUE_NORMALIZER_TYPE, IGNORE_TYPE, LOG_TRANSFORMATION_NORMALIZER_TYPE, MARKER_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE, MARKER_MEAN_VARIANCE_NORMALIZER_TYPE, MARKUS_TYPE, MAX_TYPE, MEAN_TYPE, MEDIAN_TYPE, MEDUSA_TYPE, MICROARRAY_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE, MIN_TYPE, MISSING_VALUE_NORMALIZER_TYPE, MISSING_VALUES_FILTER_TYPE, MRA_TYPE, NETBOOST_TYPE, parameterHash, PUDGE_TYPE, QUANTILE_NORMALIZER_TYPE, REPLACE_TYPE, SKYBASE_TYPE, SKYLINE_TYPE, SOM_CLUSTERING_TYPE, stopAlgorithm, THRESHOLD_NORMALIZER_TYPE, tmpDir, TTEST_TYPE, TWO_CHANNEL_THRESHOLD_FILTER_TYPE, ZERO_TYPE
 
Constructor Summary
FilteringAnalysis()
           
 
Method Summary
protected  int countMissing(int markerIndex)
           
 AlgorithmExecutionResults execute(java.lang.Object input)
          invokes the actual service
protected  boolean expectedType()
           
 int getAnalysisType()
           
 java.util.List<java.lang.Integer> getMarkersToBeRemoved(DSMicroarraySet input)
           
protected abstract  void getParametersFromPanel()
           
protected abstract  boolean isMissing(int arrayIndex, int markerIndex)
           
 
Methods inherited from class org.geworkbench.analysis.AbstractAnalysis
createHistory, deleteParameters, deserializeNamedParameterSet, deserializeNamedParameterSetPanel, generateHistoryForMaSetView, generateHistoryStringForGeneralDataSet, getDescription, getLabel, getLastSavedParameterSetName, getNamedParameterSet, getNamesOfStoredParameterSets, getParameterPanel, getParameters, loadSavedParameterSets, parameterSetExist, removeNamedParameter, saveParameters, scrubFilename, setDefaultPanel, setDescription, setLabel, setNamedParameterSetPanel, setParameters, update, validateParameters
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

maSet

protected DSMicroarraySet maSet

criterionOption

protected FilteringAnalysis.CriterionOption criterionOption

percentThreshold

protected double percentThreshold

numberThreshold

protected int numberThreshold

expectedTypeName

protected java.lang.String expectedTypeName
Constructor Detail

FilteringAnalysis

public FilteringAnalysis()
Method Detail

getAnalysisType

public int getAnalysisType()

execute

public AlgorithmExecutionResults execute(java.lang.Object input)
Description copied from interface: Analysis
invokes the actual service

Parameters:
input - input dataset
Returns:
Results of algorithm execution

getParametersFromPanel

protected abstract void getParametersFromPanel()

expectedType

protected boolean expectedType()

getMarkersToBeRemoved

public java.util.List<java.lang.Integer> getMarkersToBeRemoved(DSMicroarraySet input)

isMissing

protected abstract boolean isMissing(int arrayIndex,
                                     int markerIndex)

countMissing

protected int countMissing(int markerIndex)