@Override
public DataSet processData(DataSet input) {
List<Datum> temp = input.getDataOfType(DistanceMatrix.class);
if (temp.size() != 1) {
throw new IllegalArgumentException(
"RemoveNaNFromDistanceMatrixPlugin: preProcessParameters: Must select one Distance Matrix");
}
DistanceMatrix origMatrix = (DistanceMatrix) temp.get(0).getData();
String origName = temp.get(0).getName();
TaxaList taxa = origMatrix.getTaxaList();
int numTaxa = taxa.numberOfTaxa();
BitSet[] whichNaN = new BitSet[numTaxa];
for (int t = 0; t < numTaxa; t++) {
whichNaN[t] = new OpenBitSet(numTaxa);
}
for (int x = 0; x < numTaxa; x++) {
for (int y = x; y < numTaxa; y++) {
if (Double.isNaN(origMatrix.getDistance(x, y))) {
whichNaN[x].fastSet(y);
whichNaN[y].fastSet(x);
}
}
}
List<Integer> taxaToRemove = new ArrayList<>();
long highestCount = -1;
while (highestCount != 0) {
highestCount = 0;
int highestTaxon = -1;
for (int t = 0; t < numTaxa; t++) {
long currentCount = whichNaN[t].cardinality();
if (currentCount > highestCount) {
highestCount = currentCount;
highestTaxon = t;
}
}
if (highestCount != 0) {
taxaToRemove.add(highestTaxon);
for (int t = 0; t < numTaxa; t++) {
whichNaN[t].fastClear(highestTaxon);
whichNaN[highestTaxon].fastClear(t);
}
}
}
if (!taxaToRemove.isEmpty()) {
int newNumTaxa = numTaxa - taxaToRemove.size();
int[] origIndex = new int[newNumTaxa];
TaxaListBuilder builder = new TaxaListBuilder();
int count = 0;
for (int t = 0; t < numTaxa; t++) {
if (!taxaToRemove.contains(t)) {
builder.add(taxa.get(t));
origIndex[count++] = t;
}
}
TaxaList newTaxaList = builder.build();
double[][] result = new double[newNumTaxa][newNumTaxa];
for (int x = 0; x < newNumTaxa; x++) {
for (int y = x; y < newNumTaxa; y++) {
result[x][y] = result[y][x] = origMatrix.getDistance(origIndex[x], origIndex[y]);
}
}
DistanceMatrix resultMatrix = new DistanceMatrix(result, newTaxaList);
return new DataSet(new Datum(origName + " with no NaN", resultMatrix, null), this);
} else {
return input;
}
}
public DataSet performFunction(DataSet input) {
List data = input.getDataSet();
int numSaveFiles = 0;
if (mySaveFiles != null) {
numSaveFiles = mySaveFiles.length;
}
if ((numSaveFiles != 0) && (numSaveFiles != 1) && (numSaveFiles != data.size())) {
throw new IllegalStateException(
"ExportMultiplePlugin: performFunction: number of save files should be either 0, 1 or number of input data sets.");
}
if ((myFileTypes != null) && (myFileTypes.length != 0)) {
if ((myFileTypes.length != 1) && (myFileTypes.length != data.size())) {
throw new IllegalStateException(
"ExportMultiplePlugin: performFunction: number of files types should be either 0, 1 or number of input data sets.");
}
}
for (int i = 0, n = data.size(); i < n; i++) {
Datum datum = (Datum) data.get(i);
DataSet current = new DataSet(datum, input.getCreator());
if (numSaveFiles == 0) {
myExportPlugin.setSaveFile(datum.getName());
} else if (numSaveFiles == 1) {
String temp;
if (data.size() == 1) {
temp = mySaveFiles[0];
} else {
temp = mySaveFiles[0].replaceFirst("\\.", (i + 1) + ".");
if (temp.length() == mySaveFiles[0].length()) {
temp = mySaveFiles[0] + (i + 1);
}
}
myExportPlugin.setSaveFile(temp);
} else {
myExportPlugin.setSaveFile(mySaveFiles[i]);
}
if ((myFileTypes == null) || (myFileTypes.length == 0)) {
// do nothing
} else if (myFileTypes.length == 1) {
myExportPlugin.setAlignmentFileType(myFileTypes[0]);
} else {
myExportPlugin.setAlignmentFileType(myFileTypes[i]);
}
DataSet filename = myExportPlugin.performFunction(current);
myLogger.info(
"Datum: "
+ datum.getName()
+ " Written to: "
+ filename.getDataOfType(String.class).get(0).getData());
}
return null;
}