Package org.broad.igv.data.expression

Examples of org.broad.igv.data.expression.ExpressionFileParser

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            if (!checkSize(locator)) {
                return;
            }
        }

        ExpressionFileParser parser = null;
        ExpressionDataset ds = null;
        parser = new ExpressionFileParser(locator, null, genome);
        ds = parser.createDataset();
        if (ds.isEmpty()) {
            String message = "The probes in the file <br>&nbsp;&nbsp;&nbsp;" + locator.getPath() + "<br>" +
                    "could not be mapped to genomic positions.  This can be corrected by specify a probe mapping<br>" +
                    "file from the Preferences window (Probes tab), or by specifing the genomic positions in the<br>" +
                    "expression data file.  Please see the user guide for more details.";
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        String input = "formatexp " + inputFile + " " + outputFile;
        igvTools.run(input.split("\\s+"));
        Genome genome = TestUtils.loadGenome();

        ExpressionFileParser parser = new ExpressionFileParser(new ResourceLocator(outputFile), null, genome);
        Dataset ds = parser.createDataset();
        assertEquals(10, ds.getChromosomes().length);
    }
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    }

    @BeforeClass
    public static void setUpClass() throws Exception {
        AbstractHeadlessTest.setUpClass();
        ExpressionFileParser parser = new ExpressionFileParser(new File(file), null, genome);

        dataset = parser.createDataset();
    }
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        outputFile.deleteOnExit();

        ExpressionFormatter formatter = new ExpressionFormatter();
        formatter.convert(inputFile, outputFile, ExpressionFormatter.FileType.GCT);

        ExpressionFileParser parser = new ExpressionFileParser(new ResourceLocator(outputPath), null, genome);
        Dataset ds = parser.createDataset();
        assertTrue(ds.getDataMax() > 0);
        assertTrue(ds.getDataMin() < 0);
        //Should this be true?
        //assertTrue(ds.isLogNormalized());
    }
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Related Classes of org.broad.igv.data.expression.ExpressionFileParser

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  • org.broad.igv.preprocess.FeatureDatasetTest
  • org.broad.igv.tools.converters.ExpressionFormatterTest
  • org.broad.igv.tools.IGVToolsTest
  • org.broad.igv.track.TrackLoader
  • org.broad.igv.ui.util.MagetabSignalDialog
  • org.broad.igv.util.ResourceLocator
  • org.broad.igv.exceptions.ParserException
  • java.io.BufferedReader
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