/**
* Copy from the copy method in StructUtil. Did not want to drag that code in. maybe this actually
* should go to struct.
*
* @param from
* @param to
* @param excludes
* @return
* @throws Exception
*/
public static <T extends struct> T xcopy(struct from, T to, String... excludes) throws Exception {
Arrays.sort(excludes);
for (Field f : from.fields()) {
if (Arrays.binarySearch(excludes, f.getName()) >= 0) continue;
Object o = f.get(from);
if (o == null) continue;
Field tof = to.getField(f.getName());
if (tof != null)
try {
tof.set(to, Converter.cnv(tof.getGenericType(), o));
} catch (Exception e) {
System.out.println(
"Failed to convert "
+ f.getName()
+ " from "
+ from.getClass()
+ " to "
+ to.getClass()
+ " value "
+ o
+ " exception "
+ e);
}
}
return to;
}
/**
* This function returns a map whose entries hold the coordinates of the sequence as keys and the
* coordinates of the target sequences as values.</br> If a coordinate in sequence corresponds to
* a gap in another sequence, then -1 is assigned to that position.</br> For example suppose we
* have the sequences:</br> seq1: AAT-GCT-TCG</br> seq2: G--C-CTCT-C</br> seq3: A-T--GT-AG-</br>
* Then, if we wish to find the mapping of seq1's coordinates to seq2's coordinates, this will
* give us: 0 -> 0, 1 -> -1, 2 -> -1, 3 -> -1, 4 -> 2, 5 -> 3, 6 -> 5, 7 -> -1, 8 -> 6.</br> Also,
* if we wish to find the mapping of seq1's coordinates to seq2's and seq3's coordinates, this
* will give us: 0 -> {0, 0}, 1 -> {-1, -1}, 2 -> {-1, 1}, 3 -> {-1, -1}, 4 -> {2, 2}, 5 -> {3,
* 3}, 6 -> {5, 4}, 7 -> {-1, 5}, 8 -> {6, -1}.
*
* @param <T> This could be either the serial number of the sequence (valid range: [0,
* sequences.length-1]) or the sequence names
* @param <E>
* @param seqID The sequence ID (either serial number or name) which we wish to map</br> Note that
* the valid range of serial numbers is [0, sequences.length-1]
* @param targetSeqIDs The (target) sequences IDs (either serial numbers or names)
* @return A map whose keys are the sequence coordinates and values the corresponding coordinates
* of the target sequences
* @throws IllegalArgumentException
* @see GappedAlignmentString
*/
public <T extends Object> Map mapSeqCoords2SeqsCoords(
T generic_seqID, Vector<T> generic_targetSeqIDs)
throws IllegalArgumentException, IndexOutOfBoundsException {
GappedAlignmentString gas_seq;
GappedAlignmentString[] gas_targetSeqs;
String[] speciesNames = species();
// Check if generic_seqID is mistakenly included in the generic_targetSeqIDs set
if (generic_targetSeqIDs.contains(generic_seqID)) generic_targetSeqIDs.remove(generic_seqID);
if (generic_targetSeqIDs.size() + 1 > speciesNames.length)
throw new IndexOutOfBoundsException("You entered more sequences than are in the file.");
Map map = new HashMap();
// Check whether sequence IDs are inputed as serial numbers or as names
String seqsClassName = generic_seqID.getClass().getSimpleName();
// if( generic_seqID.getClass() instanceof java.lang.Integer )
// System.out.println("XAXA");
if (seqsClassName.equals("Integer")) {
Integer seqID = (Integer) generic_seqID;
Integer[] seqIDs = generic_targetSeqIDs.toArray(new Integer[generic_targetSeqIDs.size()]);
if ((StatUtil.findMax(seqIDs).getFirst() > speciesNames.length - 1)
|| (StatUtil.findMin(seqIDs).getFirst() < 0))
throw new IndexOutOfBoundsException(
"The sequence IDs (aka, serial numbers have to lie inside"
+ " the range 0 to speciesNames.length -1");
gas_seq = getGappedAlignment(speciesNames[seqID]);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++)
gas_targetSeqs[i] = getGappedAlignment(speciesNames[seqIDs[i]]);
} else if (seqsClassName.equals("String")) {
String seqID = (String) generic_seqID;
String[] seqIDs = generic_targetSeqIDs.toArray(new String[generic_targetSeqIDs.size()]);
gas_seq = getGappedAlignment(seqID);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++) gas_targetSeqs[i] = getGappedAlignment(seqIDs[i]);
} else {
throw new IllegalArgumentException("Sequence IDs should be either of type Integer or String");
}
// Pairwise Alignment
if (gas_targetSeqs.length == 1) {
map = doMapSeq2Seq(gas_seq, gas_targetSeqs);
}
// Multiple Alignment
else {
map = doMapSeq2Seqs(gas_seq, gas_targetSeqs);
}
return map;
} // end of mapSeqCoords2SeqsCoords method