2.17.2: 2011-06-17

Class SerialSpotIntensityEventHandler

  extended by net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
All Implemented Interfaces:

public class SerialSpotIntensityEventHandler
extends Object
implements EventHandler

Event handler that extracts spot intensity information from serial BFS data files and inserts the values to a spot batcher. In the serial format there is one data file per assay. In each file there should be one data column for each channel. All data files should have the same column layout and the same number of lines. For example, file1.txt contains data for assay #1 and file2.txt contains data for assay #2. In both files the first column (index=0) has intensity for channel 1 and the second column (index=1) has intensity for channel 2.

This event handler is designed to work together with a SynchronizedSpotDataParser and will only react to SynchronizedSpotDataParser.DATA_EVENT events.

Last modified
$Date: 2010-02-01 14:30:59 +0100 (Mon, 01 Feb 2010) $

Field Summary
private  BioAssay[] assays
private  float[] ch
private  int[] chIndex
private  PositionEventHandler positionHandler
private  SpotBatcher spotBatcher
Constructor Summary
SerialSpotIntensityEventHandler(SpotBatcher spotBatcher, PositionEventHandler positionHandler, BioAssay[] assays, int[] chIndex)
          Create a new spot instensity event handler.
Method Summary
 void handleEvent(EventType eventType, Object eventData, BfsParser parser)
          Extract the spot intensity values from the data files and batch insert them using the spot batcher.
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail


private final SpotBatcher spotBatcher


private final PositionEventHandler positionHandler


private final BioAssay[] assays


private final int[] chIndex


private float[] ch
Constructor Detail


public SerialSpotIntensityEventHandler(SpotBatcher spotBatcher,
                                       PositionEventHandler positionHandler,
                                       BioAssay[] assays,
                                       int[] chIndex)
Create a new spot instensity event handler.

spotBatcher - The spot batcher that should receive the intensity data
positionHandler - The event handler that is responsible for extracting position information from the reporter annotations file
assays - An array with all assays in the same order that they appeared in the pdata file
chIndex - An array with column indexes for channel intensities, first value is the column index for channel 1. The first column has index = 0. The size of this array should match the number of channels in the experiment.
Method Detail


public void handleEvent(EventType eventType,
                        Object eventData,
                        BfsParser parser)
Extract the spot intensity values from the data files and batch insert them using the spot batcher. If all channels are empty, no data will be inserted for that spot, otherwise a null value will be inserted for the missing channels. The parser will treat invalid values as empty columns.

Specified by:
handleEvent in interface EventHandler
eventType - The type of event. See the parser documentation for more information about the event types it generates
eventData - The data that is associated with the event
parser - The parser that is resposible for parsing the file

2.17.2: 2011-06-17