{
final File file = pageGeneData.getSelectedFile();
if (file != null){
if (controller != null)
{
CsvReader reader = (CsvReader) new CsvReaderFactory().getReader(session, file);
try
{
reader.readHeader(task);
SeriesFilterSettingsEditor settingsEditor = reader.getSettingsEditor();
if (settingsEditor != null)
{
String title = "Select settings for gene expresion data";
final SeriesFilterSettingsDialog dialog = new SeriesFilterSettingsDialog(session.getMainWindow(), settingsEditor, title);
class DialogRunner implements Runnable
{
private boolean approved = false;
@Override
public void run()
{
approved = dialog.showDialog();
}
}
DialogRunner runner = new DialogRunner();
try
{
SwingUtilities.invokeAndWait(runner);
}
catch (InterruptedException e)
{
e.printStackTrace();
}
catch (InvocationTargetException e)
{
e.printStackTrace();
}
if (!runner.approved)
return;
settingsEditor.settingsApproved();
}
Core.getProcessManager().showDialog();
//ImportConfiguration config = reader.getConfig();
//config.setColumnTypes(new String[]{"ignore","ids","ignore","ignore","values"});
reader.readData(task);
if (reader.getSeries() != null) {
seriesRegistry.registerSeries(reader.getSeries());
LinearColorMapper colorMapper = new LinearColorMapper(new Color[]{Color.BLUE,Color.WHITE,Color.RED} );
DefaultMapping mapping = new DefaultMapping(controller, "UDIS", BasicProteinComponentUI.BACKGROUNDCOLOR_MAPPING_POINT,colorMapper);
SeriesMappingConfiguration mappingConfig = new SeriesMappingConfiguration(DoubleVector.class, reader.getSeries());
mappingConfig.setSelectedSamples(reader.getSeries().getSample(0));
mappingConfig.setMappingTargetTranslator(controller.getMappingModel().createExternalIdentifierTranslator("NCBI-GeneID"));
SeriesMappingValueProvider seriesMappingValueProvider = new SeriesMappingValueProvider(session, mappingConfig, controller.getMappingTargetTranslators());
mapping.setValueProvider(seriesMappingValueProvider);