/**
* Matrix for protein distance
*
* @param matrixName "<code>BLOSUM45</code>", "<code>BLOSUM62</code>", "<code>BLOSUM80</code>"
* etc.
* @throws InvalidParamsException exception when invalid parameters.
* @throws IOException exception when IO goes wrong
*/
public ProteinScoringMatrix(String matrixName) throws InvalidParamsException, IOException {
final String mat = matrixName.toUpperCase(Locale.getDefault());
final int len = Protein.values().length;
mScores = new int[len][];
// C# restrictions
for (int i = 0; i < len; i++) {
mScores[i] = new int[len];
}
final String res = "com/rtg/mode/" + mat;
try (InputStream in = Resources.getResourceAsStream(res)) {
if (in == null) {
throw new MissingResourceException(
"Could not find:" + res, ProteinScoringMatrix.class.getName(), res);
}
try (BufferedReader re = new BufferedReader(new InputStreamReader(in))) {
try {
parse(re);
} catch (final IOException | NumberFormatException e) {
throw new MissingResourceException(
"Malformed resource: " + res + " message: " + e.getMessage(),
ProteinScoringMatrix.class.getName(),
res);
}
final String resProps = "com/rtg/mode/" + mat + ".properties";
try (final InputStream inProps = Resources.getResourceAsStream(resProps)) {
if (inProps == null) {
throw new MissingResourceException(
"Could not find:" + resProps, ProteinScoringMatrix.class.getName(), resProps);
}
final Properties pr = new Properties();
try {
pr.load(inProps);
} catch (final IOException e) {
throw new InvalidParamsException(
ErrorType.PROPS_LOAD_FAILED, "Matrix", resProps, e.getMessage());
} catch (final IllegalArgumentException e) {
throw new InvalidParamsException(ErrorType.PROPS_INVALID, "Matrix", resProps);
}
mK = getDouble(mat, pr, "K");
mLogK = Math.log(mK);
mH = getDouble(mat, pr, "H");
mLambda = getDouble(mat, pr, "LAMBDA");
mHit = getDouble(mat, pr, "HIT");
mMiss = getDouble(mat, pr, "MISS");
mGap = getDouble(mat, pr, "GAP");
mExtend = getDouble(mat, pr, "EXTEND");
mExpected = getDouble(mat, pr, "EXPECTED");
mMax = findMax();
}
}
}
assert integrity();
}
private static Tester getTesterForFile(String filename, String[] glossar, Language language) {
File inF = new File(url, filename);
File outF = new File(url, "out." + filename.substring(0, filename.indexOf('.')) + ".xml");
PrintStream output = null;
BufferedReader input = null;
try {
input = new BufferedReader(new InputStreamReader(new FileInputStream(inF)));
StringBuilder stringBuilder = new StringBuilder();
String tmp = null;
while ((tmp = input.readLine()) != null) {
stringBuilder.append(tmp);
stringBuilder.append('\n');
}
String whole = stringBuilder.toString();
if (!outF.exists()) outF.createNewFile();
output = new PrintStream(outF);
// Do actual checking
String[] lines = whole.split(RegEx.Newline);
int[] tmpLevels = new int[lines.length - 1];
String[] tmpHadings = new String[tmpLevels.length], tmpTexts = new String[tmpLevels.length];
for (int i = 1; i < lines.length; i++) {
String[] split = lines[i].split("\",\"");
tmpLevels[i - 1] = Integer.parseInt(split[0].substring(1));
tmpHadings[i - 1] = split[1];
tmpTexts[i - 1] =
split[2].substring(
0, split[2].length() - 1); // Take the whole string, except of the last char
}
Tester tester =
new Tester(
output,
tmpLevels,
tmpHadings,
tmpTexts,
glossar,
language,
url + "rules.xml",
url + "rules.xsd");
return tester;
} catch (IOException | NumberFormatException | ArrayIndexOutOfBoundsException e) {
e.printStackTrace();
return null;
}
}
@Override
protected Application configure() {
faker = new Faker();
final Configuration configuration;
try {
configuration = new Configuration(CONFIG);
} catch (IOException | NumberFormatException e) {
System.out.println("Properties error:");
System.out.println(e.getMessage());
System.exit(1);
return null;
}
final AccountServiceImpl accountService;
try {
accountService =
new AccountServiceImpl(
configuration.getDbName(),
configuration.getDbHost(),
configuration.getDbPort(),
configuration.getDbUsername(),
configuration.getDbPassword());
} catch (SQLException | IOException e) {
e.printStackTrace();
System.exit(1);
return null;
}
final ResourceConfig config = new ResourceConfig(Session.class, Users.class);
config.register(new AccountServiceAbstractBinder(accountService));
final HttpServletRequest httpServletRequest = mock(HttpServletRequest.class);
final HttpSession httpSession = mock(HttpSession.class);
final String sessionId = faker.lorem().fixedString(15);
Mockito.when(httpServletRequest.getSession()).thenReturn(httpSession);
Mockito.when(httpSession.getId()).thenReturn(sessionId);
config.register(new ServletAbstractBinder(httpServletRequest));
return config;
}
