/*
* add the given vertex info into this vertex
* combine name and weights
*/
public void concatVertex(SeqVertex vertex, Double w, int lastRealID) {
int prevLen = getName().length();
setName(getName() + vertex.getName());
_weights.add(w);
_weights.addAll(vertex.getWeights());
// System.out.println(toStringWeights());
Vector<Integer> newV = new Vector<Integer>();
if (vertex.getID() <= lastRealID) {
newV.add(vertex.getID());
_prevVerticesID.add(newV);
}
_prevVerticesID.addAll(vertex.getPrevVerIDs());
if (vertex.getDegenerativeFreq().size() > 0) {
// System.err.println(vertex.getID()+":"+vertex.getDegenerativeFreq());
// System.err.println(vertex.getID()+":"+vertex.getDegenerativeLocations());
// System.err.println(vertex.getID()+":"+vertex.getDegenerativeLetters());
// System.err.println(getID()+":"+getName());
// System.err.println(prevLen);
_degenerativeLocations.add(prevLen + 1);
_degenerativeFreq.addAll(vertex.getDegenerativeFreq());
_degenerativeLetters.addAll(vertex.getDegenerativeLetters());
}
}
/**
* add the ver id from the vToRemove to this vertex previous ids
*
* @param vToKeep
* @param vToRemove
*/
public void addToPrevIDs(SeqVertex vToKeep, SeqVertex vToRemove, int lastRealID) {
if (_prevVerticesID.isEmpty()) {
Vector<Integer> thisV = new Vector<Integer>();
if (vToKeep.getID() >= lastRealID) thisV.add(vToKeep.getID());
if (vToRemove.getID() >= lastRealID) thisV.add(vToRemove.getID());
if (!vToKeep.getPrevVerIDs().isEmpty()) thisV.addAll(vToKeep.getPrevVerIDs().firstElement());
if (!vToRemove.getPrevVerIDs().isEmpty())
thisV.addAll(vToRemove.getPrevVerIDs().firstElement());
_prevVerticesID.add(thisV);
} else {
assert (true);
}
}
public void addIDsAsFirstPrevIDs(Collection<SeqVertex> vWithL, int lAST_REAL_ID) {
Vector<Integer> prevIDs = new Vector<Integer>();
for (SeqVertex v : vWithL) {
int vid = v.getID();
if (vid >= 0)
if (vid <= lAST_REAL_ID) prevIDs.add(vid);
else if (!v.getPrevVerIDs().isEmpty()) {
prevIDs.addAll(v.getPrevVerIDs().get(0));
v.getPrevVerIDs().remove(0);
}
}
_prevVerticesID.add(prevIDs);
}