OpenBISScreeningML.java

                featureVectors.get(featureVectors.size() - 1).getFeatureNames();
        final Object[][][] result = new Object[3][][];
        if (featureVectors.isEmpty())
        {
            return result;
        }
        int numberOfRows = 0;
        for (FeatureVectorDataset fvds : featureVectors)
        {
            numberOfRows += fvds.getFeatureVectors().size();
        }
        result[0] = new Object[numberOfRows][featureNameList.size()];
        result[1] = new Object[numberOfRows][13];
        int resultIdx = 0;
        for (FeatureVectorDataset fvds : featureVectors)
        {
            final FeatureVectorDatasetReference datasetRef = fvds.getDataset();
            for (FeatureVector f : fvds.getFeatureVectors())
            {
                arraycopy(f.getValues(), result[0][resultIdx]);
                final Object[] annotations =
                        new Object[]
                            { createPlateWellDescription(datasetRef.getPlate(), f),
                                    datasetRef.getPlate().getAugmentedCode(),
                                    datasetRef.getPlate().getPermId(),
                                    datasetRef.getPlate().tryGetSpaceCode(),
                                    datasetRef.getPlate().getPlateCode(),
                                    f.getWellPosition().getWellRow(),
                                    f.getWellPosition().getWellColumn(),
                                    datasetRef.getExperimentIdentifier().getAugmentedCode(),
                                    datasetRef.getExperimentIdentifier().getPermId(),
                                    datasetRef.getExperimentIdentifier().getSpaceCode(),
                                    datasetRef.getExperimentIdentifier().getProjectCode(),
                                    datasetRef.getExperimentIdentifier().getExperimentCode(),
                                    datasetRef.getDatasetCode(), };
                System.arraycopy(annotations, 0, result[1][resultIdx], 0, annotations.length);
                resultIdx++;
            }
        }
        result[2] = new Object[featureNameList.size()][1];
        for (int i = 0; i < featureNameList.size(); ++i)
        {
            result[2][i][0] = featureNameList.get(i);
        }
        return result;
    }

    //
    // Helper methods
    //

    private static void arraycopy(double[] src, Object[] dest)
    {
        for (int i = 0; i < dest.length; ++i)
        {
            dest[i] = src[i];
        }
    }

    private static String createPlateWellDescription(FeatureVectorWithDescription f)
    {
        return createPlateWellDescription(f.getDatasetWellReference().getPlate(), f
                .getWellPosition().getWellRow(), f.getWellPosition().getWellColumn());
    }

    private static String createPlateWellDescription(PlateIdentifier p, FeatureVector f)
    {
        return createPlateWellDescription(p, f.getWellPosition().getWellRow(), f.getWellPosition()
                .getWellColumn());
    }

    private static String createPlateWellDescription(PlateIdentifier p, int row, int col)
    {
        return p.getPlateCode() + ":" + translateRowNumberIntoLetterCode(row) + col;
    }

    /**
     * Translates a row number into letter code. Thus, 1 -> A, 2 -> B, 26 -> Z, 27 -> AA, 28 -> AB,
     * etc.
     */
    private static String translateRowNumberIntoLetterCode(int rowNumber)
    {
        int rowIndex = rowNumber - 1;
        String code = "";
        while (rowIndex >= 0)
        {
            code = (char) (rowIndex % 26 + 'A') + code;
            rowIndex = rowIndex / 26 - 1;
        }
        return code;
    }

    private static void checkLoggedIn()
    {
        if (openbis == null)
        {
            if (Login.OPENBIS_TOKEN_FILE.exists())
            {
                BufferedReader br = null;
                try
                {
                    br = new BufferedReader(new FileReader(Login.OPENBIS_TOKEN_FILE));
                    final String token = br.readLine();
                    br.close();
                    br = new BufferedReader(new FileReader(Login.OPENBIS_SERVER_URL_FILE));
                    final String serverUrl = br.readLine();
                    br.close();
                    br = null;
                    openbis = ScreeningOpenbisServiceFacadeFactory.tryCreate(token, serverUrl);
                    if (openbis == null)
                    {
                        throw new RuntimeException("Login failed.");
                    }
                    init();
                } catch (IOException ex)
                {
                    if (openbis == null)
                    {
                        throw new RuntimeException("Login failed.", ex);
                    }
                } finally
                {
                    if (br != null)
                    {
                        try
                        {
                            br.close();
                        } catch (IOException ex)
                        {
                            // Silence this.
                        }
                    }
                }
            }
            if (openbis == null)
            {
                throw new RuntimeException("Not logged in.");
            }
        }
    }
}