/*
* #%L
* gitools-ui-app
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.ui.app.fileimport.wizard.text;
import org.apache.commons.io.IOUtils;
import org.gitools.api.PersistenceException;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.resource.IResource;
import org.gitools.api.resource.ResourceReference;
import org.gitools.heatmap.Heatmap;
import org.gitools.matrix.model.MatrixLayer;
import org.gitools.matrix.model.MatrixLayers;
import org.gitools.matrix.model.hashmatrix.HashMatrix;
import org.gitools.matrix.model.matrix.AnnotationMatrix;
import org.gitools.ui.app.commands.CommandLoadFile;
import org.gitools.ui.app.fileimport.wizard.text.reader.FlatTextImporter;
import org.gitools.ui.app.fileimport.wizard.text.reader.ReaderAssistant;
import java.util.concurrent.CancellationException;
import static org.gitools.api.matrix.MatrixDimensionKey.COLUMNS;
import static org.gitools.api.matrix.MatrixDimensionKey.ROWS;
public class CommandConvertAndLoadCsvFile extends CommandLoadFile {
private final FlatTextImporter reader;
public CommandConvertAndLoadCsvFile(FlatTextImporter reader) {
super(reader.getLocator().getURL().toString());
this.reader = reader;
}
@Override
public boolean isConfigurable() {
return false;
}
@Override
protected IResource loadResource(IProgressMonitor progressMonitor) {
try {
reader.setPreviewMode(false);
if (reader.getFileHeaders().size() < 3) {
throw new PersistenceException("At least 3 fields expected on one line.");
}
ReaderAssistant assistant = reader.getReaderAssistant();
MatrixLayer[] layers = assistant.getHeatmapLayers();
HashMatrix resultsMatrix = new HashMatrix(new MatrixLayers<>(layers), ROWS, COLUMNS);
AnnotationMatrix rowAnnMatrix = new AnnotationMatrix();
AnnotationMatrix colAnnMatrix = new AnnotationMatrix();
// read the file body
while ((reader.readNext())) {
if (progressMonitor.isCancelled()) {
throw new CancellationException();
}
// Write the read line into the Matrix
assistant.fillMatrixAndAnnotations(resultsMatrix, rowAnnMatrix, colAnnMatrix);
}
reader.close();
progressMonitor.info("Data loaded - preparing Heatmap");
Heatmap h = new Heatmap(resultsMatrix);
h.getRows().setAnnotationsReference(new ResourceReference<AnnotationMatrix>(h.getRows().toString().toLowerCase()+"annotations", rowAnnMatrix));
h.getColumns().setAnnotationsReference(new ResourceReference<AnnotationMatrix>(h.getColumns().toString().toLowerCase()+"annotations", colAnnMatrix));
return h;
} catch (Exception e) {
throw new PersistenceException(e);
} finally {
IOUtils.closeQuietly(reader);
}
}
}