/**
* Aligns two sequences by Needleman-Wunsch (global)
*
* @param s1 sequene #1 ({@link Read})
* @param s2 sequene #2 ({@link Read})
* @param matrix scoring matrix ({@link Matrix})
* @param o open gap penalty
* @param e extend gap penalty
* @return alignment object contains the two aligned sequences, the alignment score and alignment
* statistics
* @see Read
* @see Matrix
*/
public static Alignment align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) {
float[][] scores = matrix.getScores();
Sequence _s1;
Sequence _s2;
/*
* Commented out this stupid sequence switching. Sequence 1 should STAY sequence 1!
*/
// if (s1.length() < s2.length()) {
// _s1 = s2;
// _s2 = s1;
// } else {
_s1 = s1;
_s2 = s2;
// }
int m = _s1.length() + 1;
int n = _s2.length() + 1;
byte[] pointers = new byte[m * n];
short[] lengths = new short[m * n];
// Initializes the element (0,0) of the traceback matrix to STOP.
pointers[0] = Directions.STOP;
// Initializes the boundaries of the traceback matrix.
for (int i = 1, k = n; i < m; i++, k += n) {
pointers[k] = Directions.UP;
lengths[k] = (short) i;
}
for (int j = 1; j < n; j++) {
pointers[j] = Directions.LEFT;
lengths[j] = (short) j;
}
Cell cell = construct(_s1, _s2, scores, o, e, pointers, lengths);
Alignment alignment = traceback(_s1, _s2, matrix, pointers, cell, lengths);
alignment.setMatrix(matrix);
alignment.setOpen(o);
alignment.setExtend(e);
alignment.setName1(_s1.getId());
alignment.setName2(_s2.getId());
alignment.setOriginalSequence1(_s1);
alignment.setOriginalSequence2(_s2);
return alignment;
}
/**
* Get the list of ids of sequences in this sequence database
*
* @return the list of sequence ids.
*/
public Set<Integer> getSequenceIDs() {
Set<Integer> set = new HashSet<Integer>();
for (Sequence sequence : getSequences()) {
set.add(sequence.getId());
}
return set;
}
/**
* Actually gets the next id Gets the object of type ID from the database with the specific name.
* Then increment the id value and returns. If object does not exist, creates t.
*
* @param idName
* @return
*/
@SuppressWarnings("unchecked")
private long getNextId(String className) {
ODB odb = getOdb();
Objects objects =
odb.getObjects(new CriteriaQuery(Sequence.class, Where.equal("className", className)));
if (objects.isEmpty()) {
Sequence sequence = new Sequence();
sequence.setClassName(className);
sequence.setId(1L);
odb.store(sequence);
return 1L;
}
Sequence sequence = (Sequence) objects.getFirst();
sequence.increment();
odb.store(sequence);
return sequence.getId();
}
/**
* Get a string representation of this sequence database
*
* @return the string representation
*/
@Override
public String toString() {
StringBuilder r = new StringBuilder();
for (Sequence sequence : sequences) {
r.append(sequence.getId());
r.append(": ");
r.append(sequence.toString());
r.append('\n');
}
return r.toString();
}
/**
* It adds a sequence from an array of string that we have to interpret
*
* @param integers
* @param sequenceID
*/
public void addSequence(String[] integers, int sequenceID) {
long timestamp = -1;
Sequence sequence = new Sequence(sequences.size());
sequence.setID(sequenceID);
Itemset itemset = new Itemset();
int inicio = 0;
Map<Item, Boolean> counted = new HashMap<Item, Boolean>();
for (int i = inicio; i < integers.length; i++) {
if (integers[i].codePointAt(0) == '<') { // Timestamp
String value = integers[i].substring(1, integers[i].length() - 1);
timestamp = Long.parseLong(value);
itemset.setTimestamp(timestamp);
} else if (integers[i].equals("-1")) { // end of an itemset
long time = itemset.getTimestamp() + 1;
sequence.addItemset(itemset);
itemset = new Itemset();
itemset.setTimestamp(time);
} else if (integers[i].equals("-2")) { // end of a sequence
sequences.add(sequence);
} else {
// extract the value for an item
Item item = itemFactory.getItem(Integer.parseInt(integers[i]));
if (counted.get(item) == null) {
counted.put(item, Boolean.TRUE);
BitSet appearances = frequentItems.get(item);
if (appearances == null) {
appearances = new BitSet();
frequentItems.put(item, appearances);
}
appearances.set(sequence.getId());
}
itemset.addItem(item);
}
}
}