/**
* 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();
}
/**
* Gets the contents of the given resource as a string.
*
* @param resource name (classpath) of the resource.
* @return a String containing the contents of the stream
* @exception IOException if an error occurs.
*/
public static String resourceToString(final String resource) throws IOException {
final InputStream str = Resources.getResourceAsStream(resource);
if (str == null) {
throw new RuntimeException("Unable to find resource:" + resource);
}
final String res = FileUtils.streamToString(str);
str.close();
return res;
}
private void checkLoadVersion(int version) throws IOException {
final InputStream is =
Resources.getResourceAsStream("com/rtg/ml/resources/testZeroRVersion_" + version);
try (final DataInputStream dis = new DataInputStream(is)) {
final int type = dis.readInt();
assertEquals(MlPredictLoader.MlPredictType.ZERO_R.ordinal(), type);
final ZeroRBuilder.ZeroRClassifier bs = new ZeroRBuilder.ZeroRClassifier(dis);
assertEquals(version, bs.mCurrentVersion);
final StringBuilder str = bs.toString(new StringBuilder(), "", null);
final String s = str.toString();
assertTrue(s.contains("808/1007"));
}
}
/**
* Convenience method for turning a resource into a file that can be used as input.
*
* @param resource name (classpath) of the resource.
* @param file a <code>File</code> to write to
* @return a <code>File</code> containing the string content (same as <code>file</code>).
* @throws IOException if an error occurs
*/
public static File resourceToFile(final String resource, final File file) throws IOException {
try (InputStream stream = Resources.getResourceAsStream(resource)) {
return FileHelper.streamToFile(stream, file);
}
}