Package weka.filters.unsupervised.instance

Class RemoveSampleIDs

  • All Implemented Interfaces:
    Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.filters.UnsupervisedFilter
    public class RemoveSampleIDs
extends weka.filters.SimpleBatchFilter
implements weka.filters.UnsupervisedFilter
    Removes all the sample IDs listed in the specified text file (one sample ID per line).

    Valid options are: 

     -att-name
  The name of the attribute that holds the numeric DB ID.
  (default: sample_id)
     -sampleid-file
  The text file with the sample IDs to remove (one per line).
  (default: .)
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String DEFAULT_ATTNAME
      the default attribute name.
      static String DEFAULT_SAMPLEID_FILE
      the default file with sample IDs.
      protected String m_AttributeName
      the name of the attribute that holds the numeric database ID.
      protected adams.core.io.PlaceholderFile m_SampleIDFile
      the file with the sample IDs to remove.
      protected Set<String> m_SampleIDs
      the sample IDs to remove.

      • Fields inherited from class weka.filters.Filter

        m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

    • Constructor Summary

      Constructors 
      Constructor Description
      RemoveSampleIDs()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String attributeNameTipText()
      Returns the tip text for this property.
      protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
      Determines the output format based on the input format and returns this.
      String getAttributeName()
      Returns the name of the attribute containing the numeric database ID.
      weka.core.Capabilities getCapabilities()
      Returns the Capabilities of this filter.
      String[] getOptions()
      Gets the current settings of the filter.
      String getRevision()
      Returns the revision string.
      adams.core.io.PlaceholderFile getSampleIDFile()
      Returns the text file with the sample IDs to remove (one per line).
      String globalInfo()
      Returns a string describing this classifier.
      Enumeration listOptions()
      Returns an enumeration describing the available options.
      static void main​(String[] args)
      Main method for running this filter.
      protected weka.core.Instances process​(weka.core.Instances instances)
      Processes the given data (may change the provided dataset) and returns the modified version.
      String sampleIDFileTipText()
      Returns the tip text for this property.
      void setAttributeName​(String value)
      Sets the name of the attribute containing the numeric database ID.
      void setOptions​(String[] options)
      Parses a given list of options.
      void setSampleIDFile​(adams.core.io.PlaceholderFile value)
      Sets the text file with the sample IDs to remove (one per line).

      • Methods inherited from class weka.filters.SimpleBatchFilter

        allowAccessToFullInputFormat, batchFinished, hasImmediateOutputFormat, input

      • Methods inherited from class weka.filters.SimpleFilter

        reset, setInputFormat

      • Methods inherited from class weka.filters.Filter

        batchFilterFile, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

    • Field Detail

      • DEFAULT_SAMPLEID_FILE

        public static final String DEFAULT_SAMPLEID_FILE
        the default file with sample IDs.
        See Also:
        Constant Field Values

      • m_AttributeName

        protected String m_AttributeName
        the name of the attribute that holds the numeric database ID.

      • m_SampleIDFile

        protected adams.core.io.PlaceholderFile m_SampleIDFile
        the file with the sample IDs to remove.

      • m_SampleIDs

        protected Set<String> m_SampleIDs
        the sample IDs to remove.

    • Constructor Detail

      • RemoveSampleIDs

        public RemoveSampleIDs()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing this classifier.
        Specified by:
        globalInfo in class weka.filters.SimpleFilter
        Returns:
        a description of the classifier suitable for displaying in the explorer/experimenter gui

      • listOptions

        public Enumeration listOptions()
        Returns an enumeration describing the available options.
        Specified by:
        listOptions in interface weka.core.OptionHandler
        Overrides:
        listOptions in class weka.filters.Filter
        Returns:
        an enumeration of all the available options.

      • setOptions

        public void setOptions​(String[] options)
                throws Exception
        Parses a given list of options.
        Specified by:
        setOptions in interface weka.core.OptionHandler
        Overrides:
        setOptions in class weka.filters.Filter
        Parameters:
        options - the list of options as an array of string.s
        Throws:
        Exception - if an option is not supported.

      • getOptions

        public String[] getOptions()
        Gets the current settings of the filter.
        Specified by:
        getOptions in interface weka.core.OptionHandler
        Overrides:
        getOptions in class weka.filters.Filter
        Returns:
        an array of strings suitable for passing to setOptions.

      • setAttributeName

        public void setAttributeName​(String value)
        Sets the name of the attribute containing the numeric database ID.
        Parameters:
        value - the name of the attribute

      • getAttributeName

        public String getAttributeName()
        Returns the name of the attribute containing the numeric database ID.
        Returns:
        the name of the attribute

      • attributeNameTipText

        public String attributeNameTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • setSampleIDFile

        public void setSampleIDFile​(adams.core.io.PlaceholderFile value)
        Sets the text file with the sample IDs to remove (one per line).
        Parameters:
        value - the file

      • getSampleIDFile

        public adams.core.io.PlaceholderFile getSampleIDFile()
        Returns the text file with the sample IDs to remove (one per line).
        Returns:
        the file

      • sampleIDFileTipText

        public String sampleIDFileTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • getCapabilities

        public weka.core.Capabilities getCapabilities()
        Returns the Capabilities of this filter.
        Specified by:
        getCapabilities in interface weka.core.CapabilitiesHandler
        Overrides:
        getCapabilities in class weka.filters.Filter
        Returns:
        the capabilities of this object
        See Also:
        Capabilities

      • determineOutputFormat

        protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
                                             throws Exception
        Determines the output format based on the input format and returns this.
        Specified by:
        determineOutputFormat in class weka.filters.SimpleFilter
        Parameters:
        inputFormat - the input format to base the output format on
        Returns:
        the output format
        Throws:
        Exception - in case the determination goes wrong

      • process

        protected weka.core.Instances process​(weka.core.Instances instances)
                               throws Exception
        Processes the given data (may change the provided dataset) and returns the modified version. This method is called in batchFinished().
        Specified by:
        process in class weka.filters.SimpleFilter
        Parameters:
        instances - the data to process
        Returns:
        the modified data
        Throws:
        Exception - in case the processing goes wrong

      • getRevision

        public String getRevision()
        Returns the revision string.
        Specified by:
        getRevision in interface weka.core.RevisionHandler
        Overrides:
        getRevision in class weka.filters.Filter
        Returns:
        the revision

      • main

        public static void main​(String[] args)
        Main method for running this filter.
        Parameters:
        args - should contain arguments to the filter: use -h for help