@Override
public void performOperation(
AnnotatedPluginDocument[] annotatedDocuments,
ProgressListener progressListener,
Options options,
SequenceSelection sequenceSelection,
OperationCallback callback)
throws DocumentOperationException {
try {
String[] urnStrings = options.getValueAsString(URNS_OPTION_NAME).split("\n");
List<URN> validUrns = new ArrayList<URN>();
List<String> brokenUrns = new ArrayList<String>();
List<URN> missingUrns = new ArrayList<URN>();
for (String urnString : urnStrings) {
try {
String trimmedString = urnString.trim();
if (trimmedString.isEmpty()) {
continue;
}
URN urn = new URN(trimmedString);
if (DocumentUtilities.getDocumentByURN(urn) == null) {
missingUrns.add(urn);
continue;
}
validUrns.add(urn);
} catch (MalformedURNException e) {
brokenUrns.add(urnString);
}
}
if (!brokenUrns.isEmpty()) {
if (!Dialogs.showContinueCancelDialog(
"Some of the URNs you entered are invalid. They will be ignored:\n\n"
+ StringUtilities.join("\n", brokenUrns),
"Invalid URNs",
null,
Dialogs.DialogIcon.INFORMATION)) {
return;
}
}
if (!missingUrns.isEmpty()) {
if (!Dialogs.showContinueCancelDialog(
"Some of the URNs you entered cannot be found. They will be ignored:\n\n"
+ StringUtilities.join("\n", missingUrns),
"Missing URNs",
null,
Dialogs.DialogIcon.INFORMATION)) {
return;
}
}
DocumentUtilities.selectDocuments(validUrns);
} finally {
progressListener.setProgress(1.0);
}
}
/**
* Utility method for building a matrix of distances based on a calculator for each pairwise
* sequence distance
*
* @throws CannotBuildDistanceMatrixException only if
* useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable is false
*/
protected static double[][] buildDistancesMatrix(
PairwiseDistanceCalculator pairwiseDistanceCalculator,
int dimension,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable,
ProgressListener progress)
throws CannotBuildDistanceMatrixException {
double[][] distances = new double[dimension][dimension];
float tot = (dimension * (dimension - 1)) / 2;
int done = 0;
final double noDistance = -1;
double maxDistance = -1;
for (int i = 0; i < dimension; ++i) {
for (int j = i + 1; j < dimension; ++j) {
try {
distances[i][j] = pairwiseDistanceCalculator.calculatePairwiseDistance(i, j);
maxDistance = Math.max(distances[i][j], maxDistance);
} catch (CannotBuildDistanceMatrixException e) {
if (!useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) {
throw e;
}
distances[i][j] = noDistance;
}
distances[j][i] = distances[i][j];
if (progress != null) progress.setProgress(++done / tot);
}
}
if (maxDistance < 0) {
throw new CannotBuildDistanceMatrixException(
"It is not possible to compute the Tamura-Nei genetic distance "
+ "for these sequences because no pair of sequences overlap in the alignment.");
}
for (int i = 0; i < dimension; ++i) {
for (int j = i + 1; j < dimension; ++j) {
if (distances[i][j] == noDistance) {
distances[i][j] = distances[j][i] = maxDistance * 2;
}
}
}
return distances;
}
