Package adams.flow.source

Class SpectrumIdSupplier

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.ArrayProvider, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.LenientModeSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.ShallowCopySupporter<adams.flow.core.Actor>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.core.VariablesInspectionHandler, adams.db.DatabaseConnectionUser, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ArrayProvider, adams.flow.core.ErrorHandler, adams.flow.core.OutputProducer, adams.flow.source.ConditionalIdSupplier, SampleIdSource, SpectrumIdSource, Serializable, Comparable
    public class SpectrumIdSupplier
extends adams.flow.source.AbstractConditionalIdSupplier
implements SampleIdSource
    Returns spectrum IDs from the database.

    Input/output:
    - generates:
       java.lang.Integer


    Valid options are: 

    -D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to
    the console (0 = off).
    default: 0
    minimum: 0
 
    -name <java.lang.String> (property: name)
    The name of the actor.
    default: SpectrumIdSupplier
 
    -annotation <adams.core.base.BaseText> (property: annotations)
    The annotations to attach to this actor.
    default:
 
    -skip (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded
    as it is.
 
    -output-array (property: outputArray)
    Whether to output the IDs as array or one by one.
 
    -conditions <adams.db.AbstractConditions [options]> (property: conditions)
    The conditions for retrieving the data from the database.
    default: knir.db.SpectrumConditionsMulti
 
    -sample-ids (property: generateSampleIDs)
    If set to true, then sample IDs (= string) will be generated instead of
    database IDs (= integer).
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected boolean m_GenerateSampleIDs
      whether to return database IDs or sample IDs.

      • Fields inherited from class adams.flow.source.AbstractConditionalIdSupplier

        m_Conditions

      • Fields inherited from class adams.flow.source.AbstractDatabaseIdSupplier

        m_DatabaseConnection

      • Fields inherited from class adams.flow.source.AbstractIdSupplier

        m_Lenient

      • Fields inherited from class adams.flow.source.AbstractArrayProvider

        m_Index, m_OutputArray, m_Queue

      • Fields inherited from class adams.flow.core.AbstractActor

        m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

      • Fields inherited from interface adams.flow.core.Actor

        FILE_EXTENSION, FILE_EXTENSION_GZ

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void defineOptions()
      Adds options to the internal list of options.
      String generateSampleIDsTipText()
      Returns the tip text for this property.
      protected Class[] getAcceptedConditions()
      Returns the accepted classes for condition objects.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      protected adams.db.AbstractConditions getDefaultConditions()
      Returns the conditions container to use for retrieving the spectra.
      boolean getGenerateSampleIDs()
      Returns whether to read from the active or store table.
      protected ArrayList getIDs​(StringBuilder errors)
      Returns the IDs from the database.
      protected Class getItemClass()
      Returns the based class of the items.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      String globalInfo()
      Returns a string describing the object.
      void setGenerateSampleIDs​(boolean value)
      Sets whether to generate database IDs or sample IDs.

      • Methods inherited from class adams.flow.source.AbstractConditionalIdSupplier

        conditionsTipText, getConditions, setConditions

      • Methods inherited from class adams.flow.source.AbstractDatabaseIdSupplier

        doExecute, initialize, outputArrayTipText, setUpDatabaseConnection, wrapUp

      • Methods inherited from class adams.flow.source.AbstractIdSupplier

        getLenient, lenientTipText, setLenient

      • Methods inherited from class adams.flow.source.AbstractArrayProvider

        generates, getOutputArray, hasPendingOutput, output, preExecute, reset, setOutputArray

      • Methods inherited from class adams.flow.core.AbstractActor

        annotationsTipText, backupState, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, execute, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, postExecute, pruneBackup, pruneBackup, restoreState, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, silentTipText, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

      • Methods inherited from class adams.core.logging.LoggingObject

        getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

      • Methods inherited from interface adams.flow.core.Actor

        cleanUp, compareTo, destroy, equals, execute, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, sizeOf, stopExecution, stopExecution, toCommandLine, variableChanged, wrapUp

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel, setLoggingLevel

      • Methods inherited from interface adams.core.logging.LoggingSupporter

        getLogger, isLoggingEnabled

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager

      • Methods inherited from interface adams.flow.core.OutputProducer

        generates, hasPendingOutput, output

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Field Detail

      • m_GenerateSampleIDs

        protected boolean m_GenerateSampleIDs
        whether to return database IDs or sample IDs.

    • Constructor Detail

      • SpectrumIdSupplier

        public SpectrumIdSupplier()

    • 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.flow.source.AbstractConditionalIdSupplier

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the actor, which will be displayed in the GUI.
        Specified by:
        getQuickInfo in interface adams.flow.core.Actor
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class adams.flow.source.AbstractConditionalIdSupplier
        Returns:
        null if no info available, otherwise short string

      • getDefaultConditions

        protected adams.db.AbstractConditions getDefaultConditions()
        Returns the conditions container to use for retrieving the spectra.
        Specified by:
        getDefaultConditions in class adams.flow.source.AbstractConditionalIdSupplier
        Returns:
        the conditions

      • getAcceptedConditions

        protected Class[] getAcceptedConditions()
        Returns the accepted classes for condition objects.
        Overrides:
        getAcceptedConditions in class adams.flow.source.AbstractConditionalIdSupplier
        Returns:
        the accepted classes

      • getItemClass

        protected Class getItemClass()
        Returns the based class of the items.
        Overrides:
        getItemClass in class adams.flow.source.AbstractDatabaseIdSupplier
        Returns:
        the class

      • getDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
        Determines the database connection in the flow.
        Specified by:
        getDatabaseConnection in class adams.flow.source.AbstractDatabaseIdSupplier
        Returns:
        the database connection to use

      • getIDs

        protected ArrayList getIDs​(StringBuilder errors)
        Returns the IDs from the database.
        Specified by:
        getIDs in class adams.flow.source.AbstractIdSupplier
        Parameters:
        errors - for storing any error messages
        Returns:
        the IDs

      • setGenerateSampleIDs

        public void setGenerateSampleIDs​(boolean value)
        Sets whether to generate database IDs or sample IDs.
        Specified by:
        setGenerateSampleIDs in interface SampleIdSource
        Parameters:
        value - if true then sample IDs are generated

      • getGenerateSampleIDs

        public boolean getGenerateSampleIDs()
        Returns whether to read from the active or store table.
        Specified by:
        getGenerateSampleIDs in interface SampleIdSource
        Returns:
        true if the store table is used

      • generateSampleIDsTipText

        public String generateSampleIDsTipText()
        Returns the tip text for this property.
        Specified by:
        generateSampleIDsTipText in interface SampleIdSource
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.