Package org.broad.igv.data.expression

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

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        Lists.newArrayList("column1", "column2", "column3"), Pql.getColumnLabels(resultSet));
  }

  @Test
  public void testGetRowStringValues() {
    Row row = new Row();
    row.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue2));
    assertEquals(Lists.newArrayList("value1", "false", "1.02"), Pql.getRowStringValues(row));
  }
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    assertEquals(Lists.newArrayList("value1", "false", "1.02"), Pql.getRowStringValues(row));
  }

  @Test
  public void testCombineResultSet() {
    Row row1 = new Row();
    row1.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue1));

    Row row2 = new Row();
    row2.getValues().addAll(Lists.newArrayList(textValue2, booleanValue2, numberValue2));

    Row row3 = new Row();
    row3.getValues().addAll(Lists.newArrayList(textValue3, booleanValue3, numberValue3));

    ResultSet resultSet1 = new ResultSet();
    resultSet1.getColumnTypes().addAll(Lists.newArrayList(column1, column2, column3));
    resultSet1.getRows().addAll(Lists.newArrayList(row1, row2));
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        combinedResultSet.getRows().get(2).getValues());
  }

  @Test(expected = IllegalArgumentException.class)
  public void testCombineResultSet_badColumns() {
    Row row1 = new Row();
    row1.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue1));

    Row row2 = new Row();
    row2.getValues().addAll(Lists.newArrayList(textValue2, booleanValue2, numberValue2));

    Row row3 = new Row();
    row3.getValues().addAll(Lists.newArrayList(textValue3, booleanValue3));

    ResultSet resultSet1 = new ResultSet();
    resultSet1.getColumnTypes().addAll(Lists.newArrayList(column1, column2, column3));
    resultSet1.getRows().addAll(Lists.newArrayList(row1, row2));
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        Lists.newArrayList("column1", "column2", "column3"), Pql.getColumnLabels(resultSet));
  }

  @Test
  public void testGetRowStringValues() {
    Row row = new Row();
    row.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue2));
    assertEquals(Lists.newArrayList("value1", "false", "1.02"), Pql.getRowStringValues(row));
  }
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    assertEquals(Lists.newArrayList("value1", "false", "1.02"), Pql.getRowStringValues(row));
  }

  @Test
  public void testCombineResultSet() {
    Row row1 = new Row();
    row1.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue1));

    Row row2 = new Row();
    row2.getValues().addAll(Lists.newArrayList(textValue2, booleanValue2, numberValue2));

    Row row3 = new Row();
    row3.getValues().addAll(Lists.newArrayList(textValue3, booleanValue3, numberValue3));

    ResultSet resultSet1 = new ResultSet();
    resultSet1.getColumnTypes().addAll(Lists.newArrayList(column1, column2, column3));
    resultSet1.getRows().addAll(Lists.newArrayList(row1, row2));
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        combinedResultSet.getRows().get(2).getValues());
  }

  @Test(expected = IllegalArgumentException.class)
  public void testCombineResultSet_badColumns() {
    Row row1 = new Row();
    row1.getValues().addAll(Lists.newArrayList(textValue1, booleanValue1, numberValue1));

    Row row2 = new Row();
    row2.getValues().addAll(Lists.newArrayList(textValue2, booleanValue2, numberValue2));

    Row row3 = new Row();
    row3.getValues().addAll(Lists.newArrayList(textValue3, booleanValue3));

    ResultSet resultSet1 = new ResultSet();
    resultSet1.getColumnTypes().addAll(Lists.newArrayList(column1, column2, column3));
    resultSet1.getRows().addAll(Lists.newArrayList(row1, row2));
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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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