/**
* Input an instance for filtering. Ordinarily the instance is processed and made available for
* output immediately. Some filters require all instances be read before producing output.
*
* @param instance the input instance
* @return true if the filtered instance may now be collected with output().
* @throws IllegalStateException if no input format has been defined.
*/
public boolean input(Instance instance) {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (m_NewBatch) {
resetQueue();
m_NewBatch = false;
}
Instance inst = (Instance) instance.copy();
// First copy string values from input to output
copyValues(inst, true, inst.dataset(), getOutputFormat());
// Insert the new attribute and reassign to output
inst.setDataset(null);
inst.insertAttributeAt(m_Insert.getIndex());
inst.setDataset(getOutputFormat());
push(inst);
return true;
}
/**
* Processes the given data (may change the provided dataset) and returns the modified version.
* This method is called in batchFinished().
*
* @param instances the data to process
* @return the modified data
* @throws Exception in case the processing goes wrong
* @see #batchFinished()
*/
protected Instances process(Instances instances) throws Exception {
Instances result;
int i;
int n;
double[] values;
String value;
Instance inst;
Instance newInst;
// we need the complete input data!
if (!isFirstBatchDone()) setOutputFormat(determineOutputFormat(getInputFormat()));
result = new Instances(getOutputFormat());
for (i = 0; i < instances.numInstances(); i++) {
inst = instances.instance(i);
values = inst.toDoubleArray();
for (n = 0; n < values.length; n++) {
if (!m_Cols.isInRange(n) || !instances.attribute(n).isNumeric() || inst.isMissing(n))
continue;
// get index of value
if (instances.attribute(n).type() == Attribute.DATE) value = inst.stringValue(n);
else value = Utils.doubleToString(inst.value(n), MAX_DECIMALS);
values[n] = result.attribute(n).indexOfValue(value);
}
// generate new instance
if (inst instanceof SparseInstance) newInst = new SparseInstance(inst.weight(), values);
else newInst = new DenseInstance(inst.weight(), values);
// copy possible string, relational values
newInst.setDataset(getOutputFormat());
copyValues(newInst, false, inst.dataset(), getOutputFormat());
result.add(newInst);
}
return result;
}
public void buildClusterer(ArrayList<String> seqDB, double[][] sm) {
seqList = seqDB;
this.setSimMatrix(sm);
Attribute seqString = new Attribute("sequence", (FastVector) null);
FastVector attrInfo = new FastVector();
attrInfo.addElement(seqString);
Instances data = new Instances("data", attrInfo, 0);
for (int i = 0; i < seqList.size(); i++) {
Instance currentInst = new Instance(1);
currentInst.setDataset(data);
currentInst.setValue(0, seqList.get(i));
data.add(currentInst);
}
try {
buildClusterer(data);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}