if (individualDeletedMessages.isEmpty() || !entriesRange.isConnected(individualDeletedMessages.span())) {
Range<C> span = rangeSet.span(); assertEquals(expectedSpan, span); } catch (NoSuchElementException e) {
void testViewAgainstExpected(RangeSet<Integer> expected, RangeSet<Integer> view) { assertEquals(expected, view); assertEquals(expected.asRanges(), view.asRanges()); assertEquals(expected.isEmpty(), view.isEmpty()); if (!expected.isEmpty()) { assertEquals(expected.span(), view.span()); } for (int i = MIN_BOUND - 1; i <= MAX_BOUND + 1; i++) { assertEquals(expected.contains(i), view.contains(i)); assertEquals(expected.rangeContaining(i), view.rangeContaining(i)); } testEnclosing(view); if (view instanceof TreeRangeSet) { testRangesByLowerBounds((TreeRangeSet<Integer>) view, expected.asRanges()); } }
assertEquals(expected.asRanges(), subRangeSet.asRanges()); if (!expected.isEmpty()) { assertEquals(expected.span(), subRangeSet.span());
if ( data.rangeSet.isEmpty() || linesRead >= data.rangeSet.span().upperEndpoint() ) { setOutputDone();
private Range<Integer> singleReadEvidence(KmerEvidence e) { RangeSet<Integer> supportedBaseOffsets = TreeRangeSet.create(); for (int i = 0; i < e.length(); i++) { for (Integer contigKmerOffset : getContigBaseOffsetFor(lookup, e, i)) { // read kmer support is support for just the base transitions within the kmer supportedBaseOffsets.add(Range.closed(contigKmerOffset + 1, contigKmerOffset + k - 1)); } } // currently our support model only handles a single interval return supportedBaseOffsets.span(); } private Range<Integer> readPairEvidence(KmerEvidence e) {
if (individualDeletedMessages.isEmpty() || !entriesRange.isConnected(individualDeletedMessages.span())) {
if (individualDeletedMessages.isEmpty() || !entriesRange.isConnected(individualDeletedMessages.span())) {
/** * Take the complement of this space, bounded by existing lower and upper limits of the space. * This can be used as a way to represent a set of excluded ranges as a positive space. */ public IntegerSpace not() { if (_rangeset.isEmpty()) { return EMPTY; } return new IntegerSpace(_rangeset.complement().subRangeSet(_rangeset.span())); }
anchors.add(Range.closed(bp.start, bp.end + 1)); List<CigarElement> cigar = new ArrayList<CigarElement>(); int lastEndPos = anchors.span().lowerEndpoint(); for (Range<Integer> span : anchors.asRanges()) { cigar.add(new CigarElement(span.lowerEndpoint() - lastEndPos, CigarOperator.D));
final RangeConstraint<N> calculateRangeConstraint(final RangeConstraint<N> baseRangeConstraint) { if (ranges == null) { return baseRangeConstraint; } // Run through alternatives and resolve them against the base type final RangeSet<N> baseRangeSet = baseRangeConstraint.getAllowedRanges(); Verify.verify(!baseRangeSet.isEmpty(), "Base type %s does not define constraints", getBaseType()); final Range<N> baseRange = baseRangeSet.span(); final List<ValueRange> resolvedRanges = ensureResolvedRanges(ranges, baseRange); // Next up, ensure the of boundaries match base constraints final RangeSet<N> typedRanges = ensureTypedRanges(resolvedRanges, baseRange.lowerEndpoint().getClass()); // Now verify if new ranges are strict subset of base ranges if (!baseRangeSet.enclosesAll(typedRanges)) { throw new InvalidRangeConstraintException(typedRanges, "Range constraint %s is not a subset of parent constraint %s", typedRanges, baseRangeSet); } return new ResolvedRangeConstraint<>(constraint, typedRanges); }
final RangeConstraint<N> calculateRangeConstraint(final RangeConstraint<N> baseRangeConstraint) { if (ranges == null) { return baseRangeConstraint; } // Run through alternatives and resolve them against the base type final RangeSet<N> baseRangeSet = baseRangeConstraint.getAllowedRanges(); Verify.verify(!baseRangeSet.isEmpty(), "Base type %s does not define constraints", getBaseType()); final Range<N> baseRange = baseRangeSet.span(); final List<ValueRange> resolvedRanges = ensureResolvedRanges(ranges, baseRange); // Next up, ensure the of boundaries match base constraints final RangeSet<N> typedRanges = ensureTypedRanges(resolvedRanges, baseRange.lowerEndpoint().getClass()); // Now verify if new ranges are strict subset of base ranges if (!baseRangeSet.enclosesAll(typedRanges)) { throw new InvalidRangeConstraintException(typedRanges, "Range constraint %s is not a subset of parent constraint %s", typedRanges, baseRangeSet); } return new ResolvedRangeConstraint<>(constraint, typedRanges); }
final Range<Integer> span = baseLengths.getAllowedRanges().span();
final Range<Integer> span = baseLengths.getAllowedRanges().span();
Range<C> span = rangeSet.span(); assertEquals(expectedSpan, span); } catch (NoSuchElementException e) {
void testViewAgainstExpected(RangeSet<Integer> expected, RangeSet<Integer> view) { assertEquals(expected, view); assertEquals(expected.asRanges(), view.asRanges()); assertEquals(expected.isEmpty(), view.isEmpty()); if (!expected.isEmpty()) { assertEquals(expected.span(), view.span()); } for (int i = MIN_BOUND - 1; i <= MAX_BOUND + 1; i++) { assertEquals(expected.contains(i), view.contains(i)); assertEquals(expected.rangeContaining(i), view.rangeContaining(i)); } testEnclosing(view); if (view instanceof TreeRangeSet) { testRangesByLowerBounds((TreeRangeSet<Integer>) view, expected.asRanges()); } }
assertEquals(expected.asRanges(), subRangeSet.asRanges()); if (!expected.isEmpty()) { assertEquals(expected.span(), subRangeSet.span());