Package adams.data.filter

Class HeatmapThreshold

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.filter.Filter>, adams.core.SizeOfHandler, adams.data.filter.Filter<Heatmap>, Serializable, Comparable
    public class HeatmapThreshold
extends adams.data.filter.AbstractFilter<Heatmap>
    Replaces all intensity values that are either below or above a user-specified threshold, depending on the selected threshold type, using the pre-defined replacement value. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -no-id-update <boolean> (property: dontUpdateID)
    If enabled, suppresses updating the ID of adams.data.id.IDHandler data containers.
    default: false
 
    -type <ABOVE|BELOW> (property: type)
    The type of threshold to use: if BELOW then all values that fall below the 
    threshold are zeroed, if ABOVE then all values that are above the threshold 
    are zeroed.
    default: BELOW
 
    -threshold <adams.data.filter.heatmapthreshold.AbstractHeatmapThreshold> (property: threshold)
    The threshold algorithm to use.
    default: adams.data.filter.heatmapthreshold.Manual
 
    -replacement <double> (property: replacement)
    The replacement value to use.
    default: -1.0
 
    -replace-with-missing <boolean> (property: replaceWithMissing)
    If enabled, the values are replaced with missing values rather than actual 
    values.
    default: false
 
    -missing-values-handling <SKIP|REPLACE> (property: missingValuesHandling)
    Determines how missing values are handled when processing the heatmap, eg 
    whether they get skipped or always replaced.
    default: SKIP
    Version:
    $Revision$
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • m_Replacement

        protected double m_Replacement
        the replacement value.

      • m_ReplaceWithMissing

        protected boolean m_ReplaceWithMissing
        whether to replace with missing values.

    • Constructor Detail

      • HeatmapThreshold

        public HeatmapThreshold()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.data.filter.AbstractFilter<Heatmap>

      • setType

        public void setType​(HeatmapThreshold.Type value)
        Sets the type of threshold to use.
        Parameters:
        value - the type

      • getType

        public HeatmapThreshold.Type getType()
        Returns the type of threshold in use.
        Returns:
        the type

      • typeTipText

        public String typeTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setThreshold

        public void setThreshold​(AbstractHeatmapThreshold value)
        Sets the threshold algorithm to use.
        Parameters:
        value - the algorithm

      • getThreshold

        public AbstractHeatmapThreshold getThreshold()
        Returns the threshold algorithm in use.
        Returns:
        the algorithm

      • thresholdTipText

        public String thresholdTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setReplacement

        public void setReplacement​(double value)
        Sets the replacement value to use.
        Parameters:
        value - the replacement

      • getReplacement

        public double getReplacement()
        Returns the replacement value in use.
        Returns:
        the replacement

      • replacementTipText

        public String replacementTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setReplaceWithMissing

        public void setReplaceWithMissing​(boolean value)
        Sets whether to replace the values with missing values instead.
        Parameters:
        value - true if to replace with missing

      • getReplaceWithMissing

        public boolean getReplaceWithMissing()
        Returns whether to replace the values with missing values instead.
        Returns:
        true if to replace with missing

      • replaceWithMissingTipText

        public String replaceWithMissingTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • missingValuesHandlingTipText

        public String missingValuesHandlingTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • processData

        protected Heatmap processData​(Heatmap data)
        Performs the actual filtering.
        Specified by:
        processData in class adams.data.filter.AbstractFilter<Heatmap>
        Parameters:
        data - the data to filter
        Returns:
        the filtered data