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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;
}
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//
// 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());
}
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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)
{
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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.");
}