Package net.sf.basedb.util.importer.spotdata

Class SerialSpotIntensityEventHandler

java.lang.Object

net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

All Implemented Interfaces:

EventHandler

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.

Version:

2.15

Author:

Nicklas

Last modified

$Date: 2015-04-20 11:08:18 +0200 (må, 20 apr 2015) $

Field Summary

Fields

Modifier and Type	Field	Description
private final BioAssay[]	assays
private float[]	ch
private final int[]	chIndex
private final PositionEventHandler	positionHandler
private final SpotBatcher	spotBatcher

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
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 Details

spotBatcher

private final SpotBatcher spotBatcher

positionHandler

private final PositionEventHandler positionHandler

assays

private final BioAssay[] assays

chIndex

private final int[] chIndex

ch

private float[] ch

Constructor Details

SerialSpotIntensityEventHandler

public SerialSpotIntensityEventHandler(SpotBatcher spotBatcher,
 PositionEventHandler positionHandler,
 BioAssay[] assays,
 int[] chIndex)

Create a new spot instensity event handler.

Parameters:

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 Details

handleEvent

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

Parameters:

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