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/** |
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$Id$ |
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Copyright (C) 2010 Nicklas Nordborg |
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.util.importer.spotdata; |
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import net.sf.basedb.core.BioAssay; |
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import net.sf.basedb.core.SpotBatcher; |
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import net.sf.basedb.util.Values; |
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import net.sf.basedb.util.bfs.BfsParser; |
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import net.sf.basedb.util.bfs.DataParser; |
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import net.sf.basedb.util.bfs.EventHandler; |
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import net.sf.basedb.util.bfs.EventType; |
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import net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData; |
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/** |
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Event handler that extracts spot intensity information from matrix BFS |
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data files and inserts the values to a spot batcher. In the matrix format |
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there is one data file per channel. In each file there should be one data |
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column for each assay. All data files should have the same |
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column layout and the same number of lines. For example, file1.txt |
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contains data for channel 1 and file2.txt contains data for channel 2. |
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In both files the first column (index=0) has intensity for assay #1 |
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and the second column (index=1) has intensity for assay #2. |
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<p> |
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This event handler is designed to work together with a {@link SynchronizedSpotDataParser} |
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and will only react to {@link SynchronizedSpotDataParser#DATA_EVENT} events. |
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@author Nicklas |
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@version 2.15 |
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@base.modified $Date$ |
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*/ |
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public class MatrixSpotIntensityEventHandler |
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implements EventHandler |
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{ |
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private final SpotBatcher spotBatcher; |
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private final PositionEventHandler positionHandler; |
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private final BioAssay[] assays; |
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private final int[] chIndex; |
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private float[] ch; |
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/** |
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Create a new spot instensity event handler. |
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@param spotBatcher The spot batcher that should receive the intensity data |
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@param positionHandler The event handler that is responsible for extracting |
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position information from the reporter annotations file |
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@param assays An array with all assays in the same order that they |
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appeared in the pdata file |
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@param chIndex An array with file indexes for channel intensities, |
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first value is the file index for channel 1. The first file has |
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index = 0. The size of this array should match the number of channels |
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in the experiment. |
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*/ |
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public MatrixSpotIntensityEventHandler(SpotBatcher spotBatcher, |
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PositionEventHandler positionHandler, BioAssay[] assays, int[] chIndex) |
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{ |
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if (spotBatcher == null) throw new NullPointerException("spotBatcher"); |
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if (positionHandler == null) throw new NullPointerException("positionHandler"); |
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if (assays == null) throw new NullPointerException("assays"); |
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if (chIndex == null) throw new NullPointerException("chIndex"); |
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this.spotBatcher = spotBatcher; |
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this.positionHandler = positionHandler; |
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this.assays = assays; |
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this.chIndex = chIndex; |
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this.ch = new float[chIndex.length]; |
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} |
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/** |
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Extract the spot intensity values from the data files and batch insert |
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them using the spot batcher. If all channels are empty, no data will be |
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inserted for that spot, otherwise a null value will be inserted for |
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the missing channels. The parser will treat invalid values as |
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empty columns. |
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*/ |
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@SuppressWarnings("rawtypes") |
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@Override |
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public void handleEvent(EventType eventType, Object eventData, BfsParser parser) |
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{ |
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if (eventType == SynchronizedSpotDataParser.DATA_EVENT) |
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{ |
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SynchronizedData[] data = (SynchronizedData[])eventData; |
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int position = positionHandler.getCurrentPosition(); |
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for (int i = 0; i < assays.length; ++i) |
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{ |
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boolean allNaN = true; |
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for (int j = 0; j < ch.length; ++j) |
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{ |
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SynchronizedData assayData = data[chIndex[j]+1]; |
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ch[j] = Values.getFloat(assayData.getData()[i], Float.NaN); |
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allNaN &= Float.isNaN(ch[j]); |
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} |
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if (!allNaN) |
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{ |
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spotBatcher.insert(assays[i].getDataCubeColumnNo(), position, ch); |
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} |
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} |
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} |
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else if (eventType == DataParser.END_OF_FILE_EVENT) |
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{ |
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spotBatcher.flush(); |
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} |
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} |
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} |