/**
* @param gas_seq The sequence which we wish to map it against other sequence(s)
* @param gas_targetSeqs The target sequence
*/
private HashMap<Integer, Integer> doMapSeq2Seq(
GappedAlignmentString gas_seq, GappedAlignmentString[] gas_targetSeqs) {
int N = gas_seq.gappedLength();
// making map allocation more efficient
int initCapacity = (int) Math.ceil(1.5 * N);
HashMap<Integer, Integer> map = new HashMap<Integer, Integer>(initCapacity);
// When a gap position corresponds to a gap remove it from seq
HashMap<Integer, Integer> gapped2UngappedMap_seq = gas_seq.getGapped2UngappedMap();
Integer[] gapPositions_seq = gas_seq.determineGapPositions();
for (Integer e : gapPositions_seq) gapped2UngappedMap_seq.remove(e);
// When a gap position corresponds to a gap, put -1 as its value
HashMap<Integer, Integer> gapped2UngappedMap_targetSeq =
gas_targetSeqs[0].getGapped2UngappedMap();
Integer[] gapPositions_targetSeq = gas_targetSeqs[0].determineGapPositions();
for (Integer e : gapPositions_targetSeq) gapped2UngappedMap_targetSeq.put(e, -1);
Integer[] gappedPositionsNoGaps_seq =
gapped2UngappedMap_seq.keySet().toArray(new Integer[gapped2UngappedMap_seq.size()]);
for (Integer gappedPosNoGaps : gappedPositionsNoGaps_seq) {
Integer ungappedPos = gapped2UngappedMap_targetSeq.get(gappedPosNoGaps);
if (ungappedPos.equals(null)) {
ungappedPos = -1;
}
map.put(gapped2UngappedMap_seq.get(gappedPosNoGaps), ungappedPos);
}
return map;
} // end of doMapSeq2Seq method
/**
* Valid values for <tt>s1</tt> and <tt>s2</tt> are [0, ordering.size()-1]
*
* @param s1 The serial number of the sequence (<tt>s1</tt>) whose coordinate we wish to map
* against that of (<tt>s2</tt>)
* @param s2 The other sequence
* @param ugidx The ungapped coordinate of (<tt>s1</tt>)
* @return The ungapped coordinate of (<tt>s2</tt>) corresponding to <tt>ugidx</tt>
* @see GappedAlignmentString
*/
public int mapUngapped(int s1, int s2, int ugidx) throws IndexOutOfBoundsException {
if ((s1 < 0 || s1 >= ordering.size()) || (s2 < 0 || s2 >= ordering.size()))
throw new IndexOutOfBoundsException("Valid values for s1 and s2 are [0, ordering.size()-1]");
GappedAlignmentString str1 = gappedAlignments.get(ordering.get(s1));
GappedAlignmentString str2 = gappedAlignments.get(ordering.get(s2));
int gidx = str1.ungappedToGapped(ugidx);
int ugidx2 = str2.gappedToUngapped(gidx);
if (str2.isGap(gidx)) {
return -1;
}
return ugidx2;
}
/**
* Adds the sequence with name <tt>name</tt> and sequence <tt>gas</tt> to the alignment.
*
* @param name The name of the sequence to be added
* @param gas The sequence as a <tt>GappedAlignmentString</tt>
* @see GappedAlignmentString
*/
public void addGappedAlignment(String name, GappedAlignmentString gas) {
if (ordering.isEmpty()) {
gappedLength = gas.gappedLength();
} else {
if (gas.gappedLength() != gappedLength) {
throw new IllegalArgumentException(
String.format("Gapped Length %d doesn't match.", gas.gappedLength()));
}
if (ordering.contains(name)) {
throw new IllegalArgumentException(String.format("Duplicate name: %s", name));
}
}
ordering.add(name);
gappedAlignments.put(name, gas);
}