*/
public class SearchResults implements SearchResultsI
{
+ private int count;
- private List<SearchResultMatchI> matches = new ArrayList<>();
+ private ArrayList<SearchResultMatchI> matches = new ArrayList<>();
/**
* One match consists of a sequence reference, start and end positions.
* Discontiguous ranges in a sequence require two or more Match objects.
*/
- public class Match implements SearchResultMatchI
+ public class Match implements SearchResultMatchI, Comparable<SearchResultMatchI>
{
final SequenceI sequence;
{
return (sequence == seq && start <= from && end >= to);
}
+ @Override
+ public boolean adjacent(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && ((start <= from && end >= to) || (from<=(end+1) && to >=(end+1)) || (from<=(start-1) && to>=(start-1))));
+ }
+
+ @Override
+ public int compareTo(SearchResultMatchI o)
+ {
+ if (start<o.getStart())
+ {
+ return -1;
+ }
+ if (start > o.getStart())
+ {
+ return +1;
+ }
+ if (end < o.getEnd())
+ {
+ return -1;
+ }
+ if (end > o.getEnd())
+ {
+ return +1;
+ }
+ if (sequence!=o.getSequence())
+ {
+ int hashc =sequence.hashCode(),oseq=o.getSequence().hashCode();
+ return (hashc < oseq) ? -1 : 1;
+ }
+ return 0;
+ }
+
}
@Override
if (!matches.contains(m))
{
matches.add(m);
+ count++;
}
return m;
}
@Override
+ public void addResult(SequenceI seq, int[] positions)
+ {
+ /*
+ * we only increment the match count by 1 - or not at all,
+ * if the matches are all duplicates of existing
+ */
+ int beforeCount = count;
+ for (int i = 0; i < positions.length - 1; i += 2)
+ {
+ addResult(seq, positions[i], positions[i + 1]);
+ }
+ if (count > beforeCount)
+ {
+ count = beforeCount + 1;
+ }
+ }
+
+
+ @Override
+ public boolean appendResult(SequenceI sequence, int start, int end)
+ {
+
+ Match m = new Match(sequence, start, end);
+
+ boolean appending=false;
+
+ // we dynamically maintain an interval to add as we test each range in the list
+
+ int cstart=start,cend=end;
+ List<SearchResultMatchI> toRemove=new ArrayList<>();
+ for (SearchResultMatchI thatm:matches)
+ {
+ if (thatm.getSequence()==sequence)
+ {
+ if (thatm.contains(sequence,cstart,cend))
+ {
+ // found a match containing the current range. nothing else to do except report if we operated on the list
+ return appending;
+ }
+ if (thatm.adjacent(sequence, cstart, cend))
+ {
+ // update the match to add with the adjacent start/end
+ start = Math.min(m.start, thatm.getStart());
+ end = Math.max(m.end, thatm.getEnd());
+ // and check if we keep or remove the old one
+ if (thatm.getStart()!=start || thatm.getEnd()!=end)
+ {
+ toRemove.add(thatm);
+ count--;
+ cstart = start;
+ cend = end;
+ appending=true;
+ } else {
+ return false;
+ }
+ }
+ }
+ }
+ matches.removeAll(toRemove);
+ {
+ matches.add(new Match(sequence,cstart,cend));
+ count++;
+ }
+ return appending;
+ }
+ @Override
public boolean involvesSequence(SequenceI sequence)
{
final int start = sequence.getStart();
{
mfound = true;
matchStart = sequence.findIndex(m.start) - 1;
- matchEnd = m.start == m.end ? matchStart : sequence
- .findIndex(m.end) - 1;
+ matchEnd = m.start == m.end ? matchStart
+ : sequence.findIndex(m.end) - 1;
}
if (mfound)
else
{
// debug
- // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // jalview.bin.Console.errPrintln("Outwith bounds!" + matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
}
@Override
- public int getSize()
+ public int getCount()
{
- return matches.size();
+ return count;
}
@Override
}
/**
- * Two SearchResults are considered equal if they contain the same matches in
- * the same order.
+ * Two SearchResults are considered equal if they contain the same matches
+ * (Sequence, start position, end position) in the same order
+ *
+ * @see Match#equals(Object)
*/
@Override
public boolean equals(Object obj)
{
matches.addAll(toAdd.getResults());
}
+
+ @Override
+ public List<SequenceI> getMatchingSubSequences()
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ for (SearchResultMatchI match : matches)
+ {
+ SequenceI seq = match.getSequence();
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ // getSubSequence is index-base0, findIndex returns index-base1
+ seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+ seq.findIndex(match.getEnd())));
+ }
+ return seqs;
+ }
+
}