/**
* Create new test directory within the system-defined unit test master directory. The newly
* created directory will be a sub-directory of the master directory.
*
* @param dirName Directory name to be created within the master directory.
* @return Absolute path name of test directory.
*/
public static String newTestDirectory(final String dirName) {
String tempDir = UnitTestUtils.getUnitTestProperty("temp.dir");
File dir = new File(tempDir);
if (!dir.exists()) {
throw new RuntimeException("Please create directory '" + tempDir + "' for unit testing");
}
String testDirName = tempDir + "/" + dirName;
File testDir = new File(testDirName);
if (!testDir.exists()) {
testDir.mkdir();
}
return testDirName;
}
/**
* Tester for <code>IdeogramPlotPainter</code>.
*
* @author dhall
*/
public final class IdeogramPlotPainterTester extends TestCase {
// ===============================
// Constants
// ===============================
/** Name of temporary directory for storing generated ata files. This is not an absolute path. */
private static final String TEMP_DIR_NAME = "ideogram_plot_painter_test_dir";
/**
* Path to temporary directory for storing data files. It will be a subdirectory of the main unit
* test temporary directory specified by the property 'temp.dir' in 'unit_test.properties.'
*/
private static final String TEMP_DIR_PATH =
UnitTestUtils.createUnitTestDirectory(TEMP_DIR_NAME).getAbsolutePath();
/** Number of bioassays to generate in tests. */
private static final int NUM_BIO_ASSAYS = 2;
/** Number of chromosomes in tests. */
private static final int NUM_CHROMOSOMES = 5;
/** Number of experiments in tests. */
private static final int NUM_EXPERIMENTS = 2;
/** Number of array datum per chromosome in. */
private static final int NUM_DATUM_PER_CHROMOSOME = 50;
/** Length of chromosome in base pairs. */
private static final long CHROM_LENGTH = 100000000;
/** Number of cytobands. */
private static final int NUM_CYTOBANDS = 10;
// ===================================
// Test cases
// ===================================
/**
* Test paintIdeogramPlot() method.
*
* @throws Exception if something bad happens
*/
public void testPaintIdeogramPlot() throws Exception {
// Create test experiments
long gap = CHROM_LENGTH / NUM_DATUM_PER_CHROMOSOME;
ExperimentGenerator expGen = new ExperimentGenerator(gap);
Collection<Experiment> experiments = new ArrayList<Experiment>();
for (int i = 0; i < NUM_EXPERIMENTS; i++) {
Experiment exp =
expGen.newInMemoryExperiment(NUM_BIO_ASSAYS, NUM_CHROMOSOMES, NUM_DATUM_PER_CHROMOSOME);
exp.setQuantitationType(QuantitationType.COPY_NUMBER);
experiments.add(exp);
for (BioAssay ba : exp.getBioAssays()) {
ba.setColor(Color.BLUE);
}
}
for (int i = 0; i < NUM_EXPERIMENTS; i++) {
Experiment exp =
expGen.newInMemoryExperiment(NUM_BIO_ASSAYS, NUM_CHROMOSOMES, NUM_DATUM_PER_CHROMOSOME);
exp.setQuantitationType(QuantitationType.FOLD_CHANGE);
experiments.add(exp);
for (BioAssay ba : exp.getBioAssays()) {
ba.setColor(Color.RED);
}
}
// Create plot parameters
IdeogramPlotParameters params = new IdeogramPlotParameters();
for (int i = 1; i <= NUM_CHROMOSOMES; i++) {
params.add(new GenomeInterval((short) i, 1, CHROM_LENGTH));
}
params.setIdeogramSize(ChromosomeIdeogramSize.MEDIUM);
params.setNumPlotsPerRow(2);
// Create plotting panel
RasterFileTestPlotPanel panel = new RasterFileTestPlotPanel(TEMP_DIR_PATH);
// Create chromosome array data getter
InMemoryChromosomeArrayDataGetter cadg = new InMemoryChromosomeArrayDataGetter();
// Instantiate ideogram plot painter
IdeogramPlotPainter painter = new IdeogramPlotPainter(cadg);
// Create cytologial map DAO
CytologicalMapDaoImpl cDao = new CytologicalMapDaoImpl(CHROM_LENGTH, NUM_CYTOBANDS);
painter.setCytologicalMapDao(cDao);
// Create plot
painter.paintPlot(panel, experiments, params);
// Add some additional reference widgets
panel.add(
new Caption("Left", null, Orientation.HORIZONTAL, false, panel.getDrawingCanvas()),
HorizontalAlignment.LEFT_OF,
VerticalAlignment.CENTERED);
panel.add(
new Caption("Right", null, Orientation.HORIZONTAL, false, panel.getDrawingCanvas()),
HorizontalAlignment.RIGHT_OF,
VerticalAlignment.CENTERED);
// Output graphics to file
panel.toPngFile("plot-in-memory.png");
}
}