Class ExperimentExplorer


  • public class ExperimentExplorer
    extends Object
    A class for storing settings and doing work related to the experiment explorer tool in the web interface. The JSP pages that uses this class are located in the www/views/experiments/explorer directory and it's subdirectory.

    This class is used two things:

    • Storing the settings
    • Creating the queries that retrieves the data according to the settings

    Most of the settings are stored in regular ItemContext: objects. This means that they will be saved to the database when the user logs out and loaded again the next time they are needed. Each experiment explorer uses two ItemContext objects. One for storing the settings for the reporter search page and one for the view page. The reporter search settings are stored in the context SessionControl.getCurrentContext(Item.REPORTER, "explorer.id") and the view page settings are stored in SessionControl.getCurrentContext(Item.SPOTDATA, "explorer.id") where "id" is replaced by the bioassayset's id.

    Version:
    2.0
    Author:
    nicklas
    Last modified
    $Date: 2019-04-05 13:42:26 +0200 (fre, 05 apr. 2019) $
    • Field Detail

      • COLORS

        public static final String[] COLORS
        Predefined colors for annotation groups
      • defaultReporterContext

        private static final ItemContext defaultReporterContext
        The default context for the reporter search page.
      • defaultSpotContexts

        private static final Map<RawDataType,​ItemContext> defaultSpotContexts
        Stores default context for the spot data list on the view page. Different defaults for each raw data type since they can have different number of channels.
      • bioAssaySet

        private final BioAssaySet bioAssaySet
        The bioassay set we are exploring.
      • snapshotManager

        private SnapshotManager snapshotManager
        The snapshot manager that loads annotation values.
      • posCache

        private int[] posCache
      • reporterIndex

        private int reporterIndex
        The index of the current reporter on the view page.
        See Also:
        getReporterIndex()
      • positionIndex

        private int positionIndex
        The index of the curren position on the view page.
        See Also:
        getPositionIndex()
      • matchingReporters

        private int matchingReporters
        Number of reporter that match the reporter search.
      • annotationTypeIds

        private Set<Integer> annotationTypeIds
        The currently selected annotation types on the view page.
    • Constructor Detail

      • ExperimentExplorer

        private ExperimentExplorer​(BioAssaySet bioAssaySet)
        Create a new experiment explorer.
    • Method Detail

      • getExplorer

        public static ExperimentExplorer getExplorer​(BioAssaySet bioAssaySet)
        Get the existing experiment explorer for a bioassayset or create a new one if none exist yet. The returned object is cached in the SessionControl:s session settings.
        Parameters:
        bioAssaySet - The bioassay set to get an experiment explorer for
        Returns:
        An ExperimentExplorer object
      • getExperiment

        public Experiment getExperiment​(DbControl dc)
        Get the experiment that is currently beeing explored.
        Parameters:
        dc - The DbControl used for access the database
        Returns:
        The Experiment object
      • getSnapshotManager

        public SnapshotManager getSnapshotManager()
        Get the snapshot manager that is used to load annotation values.
        Since:
        2.14
      • getNumBioAssays

        public int getNumBioAssays()
        Get the number of bioassays in the bioassayset.
      • getBioAssay

        public BioAssay getBioAssay​(DbControl dc,
                                    short columnNo)
        Get the bioassay with the specified column number in the data cube. This method is useful since spot queries (see getSpotQuery(DbControl, int, int, List)) can only return the column number, but we usually want to display the name, etc.
        Parameters:
        dc - The DbControl object used to get the bioassay
        columnNo - The colum number
        Returns:
        The bioassay with the specified column number or null if no bioassay is found
      • getCacheSize

        public int getCacheSize()
        The number of reporter id'd to cache. For performance reasons the id's of the reporters matching the reporter search are cached. This means we can step forwards and backwards more quickly on the view page since we don't have to execute the reporter search each time. This method should return the same value as getMatchingReporters(DbControl) unless the cache hasn't been initialized.
        Returns:
        The size of the cache, or 0 if the cache has not been initialized
      • getNumReporters

        public int getNumReporters()
        Get the total number of unique reporters found in the bioassayset.
        See Also:
        BioAssaySet.getNumReporters()
      • getNumSpots

        public int getNumSpots()
        Get the total number of spots in the bioassayset.
        See Also:
        BioAssaySet.getNumSpots()
      • getSubContext

        public String getSubContext()
        Get the subcontext name used for the ItemContext objects related to this explorer. The name is created like this: explorer.id where id is replaced with the id of the bioassayset we are exploring.
        Returns:
        The subcontext name
      • getDefaultSpotContext

        public ItemContext getDefaultSpotContext()
        Get the default spot context that is used to initialise the actual context.
        Returns:
        An ItemContext object
      • getDefaultReporterContext

        public ItemContext getDefaultReporterContext()
        Get the default reporter context that is used to initialise the actual context.
        Returns:
        An ItemContext object
      • getAnnotationTypeIds

        public Set<Integer> getAnnotationTypeIds()
        Get the selected annotation types.
        Returns:
        A set with the id's of the selected annotation types
        Since:
        2.14
      • setAnnotationTypeIds

        public void setAnnotationTypeIds​(Collection<Integer> ids)
        Update the selected annotation types.
        Parameters:
        ids - A collection containing the id's of all annotation types that should currently be selected, all other annotation types are automatically deselected
        Since:
        2.14
      • getAnnotationTypes

        public List<AnnotationType> getAnnotationTypes​(DbControl dc,
                                                       boolean includeBioAssayAnnotations)
        Get the annotation types that are of interest in this experiment. Ie. the experimental factors of the experiment the bioassayset we are exploring belongs to. Optionally, you can also get annotations for bioassays.
        Parameters:
        dc - The DbControl for database access
        includeBioAssayAnnotations - If bioassay annotation should be included even if they are not experimental factors
        Returns:
        A list of annotation types, null may be returned if no annotation types exists
        See Also:
        Experiment.getExperimentalFactors()
      • getAnnotationSummary

        public ExperimentExplorer.AnnotationSummary getAnnotationSummary​(DbControl dc,
                                                                         AnnotationType annotationType)
        Get an AnnotationSummary object which can be used to calculate means and other values for each annotation group. When the annotation summary object is create each bioassay is placed in one annotation group based on which annotatations it have. Each annotation group is unique and is the only one with the same combination of annotation values. More than one bioassay may be placed in the same group if they are annotated with the same values.
        Parameters:
        dc - The DbControl for database access
        annotationType - The annotation type, mustn't be null
        Returns:
        An AnnotationSummary object
        See Also:
        ExperimentExplorer.AnnotationGroup.getAnnotationValues()
      • getMatchingReporters

        public int getMatchingReporters​(DbControl dc)
        Get the number of reporters matching the current reporter filter.
        Parameters:
        dc - The DbControl for database access
        Returns:
        an int of matching reporters
      • setReporterIndex

        public void setReporterIndex​(int reporterIndex)
        Set the index of the currently viewed reporter. If the index is below zero or greater than or equal to getMatchingReporters(DbControl) it is set to the nearest index.
        Parameters:
        reporterIndex - The new index
        See Also:
        getReporter(DbControl, int)
      • getReporter

        public ReporterData getReporter​(DbControl dc,
                                        int index)
        Get the reporter for the specified index. The index should be between 0 and the number of matching reporters minus 1. The returned reporter information is taken from the cloned table if that is present in the current experiment.
        Parameters:
        dc - The DbControl to use for database access
        index - The index
        Returns:
        The reporter or null if no reporter is found at the specified index
        See Also:
        getMatchingReporters(DbControl)
      • getReporterId

        public int getReporterId​(int index)
        Get the reporter id for the specified index. The index should be between 0 and the number of matching reporters minus 1. This method assumed that the reporter/position cache has already been initialized.
        Parameters:
        index - The index
        Returns:
        The internal id of the reporter, or 0 if the cache is not initialized or if the index is outside the allowed range
        Since:
        3.0
        See Also:
        getMatchingReporters(DbControl)
      • getNumPositions

        public int getNumPositions​(DbControl dc,
                                   int index)
        Get the number of unique positions the reporter of the specifed index is present in among all the bioassays in the bioassay set. The index should be between 0 and the number of matching reporters minus 1.
        Parameters:
        dc - The DbControl to use for database access
        index - The reporter index
        Returns:
        The number of positions, or 0 if the index is outside the valid range
        Since:
        2.11
        See Also:
        getReporter(DbControl, int), getMatchingReporters(DbControl)
      • getPosition

        public int getPosition​(DbControl dc,
                               int reporterIndex,
                               int positionIndex)
        Get the position number of the position specified by the given reporter and position index. For a given reporter the positions are sorted in ascending order. The reporter index should be a value between 0 and the number of matching reporter minus 1. The position index should be a value between 0 and the number of positions for the given reporter minus 1.
        Parameters:
        reporterIndex - The reporter index
        positionIndex - The position index
        Returns:
        The position number or -1 if no position can be found with the given indexes
        Since:
        2.11
        See Also:
        getMatchingReporters(DbControl), getNumPositions(DbControl, int)
      • getSpotQuery

        public DynamicSpotQuery getSpotQuery​(DbControl dc,
                                             int reporterIndex,
                                             int positionIndex,
                                             List<TableColumn> selectionList)
        Get a query returning spot data for a given reporter and position. This query is used by the view page to list the spot data for each bioassay.

        The column number is always included as the first selected property. If the SPOT_AVG is specified for positionIndex a count of the number of positions is included as the second selected property. Otherwise, the position number is included as the second selected property.

        Then, all channel intensities are selected.

        See ItemContext.getDynamicExpression(DbControl, SqlQuery, String) for more information about how to specify additional selection properties.

        Parameters:
        dc - The DbControl for database access
        reporterIndex - The index of the reporter
        positionIndex - The index of the position, or one the special values SPOT_ALL or SPOT_AVG
        selectionList - The data that the query should select
        Returns:
        A query
        Since:
        2.11
      • initReporterCache

        private void initReporterCache​(DbControl dc)