List of incAll() Examples

Examples of incAll()

org.broadinstitute.gatk.utils.collections.CountSet.incAll()
Increase (or decrease) all elements in the set by a number. @param delta the number of add (or substract if negative) to all elements. @return true if the set changed as a result of this invocation, false otherwise.

Examples of org.broadinstitute.gatk.utils.collections.CountSet.incAll()

                    else
                        previous.addAll(depth);
                }
            } else {
                final CountSet depthPlusOne = depth.clone();
                depthPlusOne.incAll(1);
                final Set<MultiSampleEdge> nextEdges = backwards ? incomingEdgesOf(v) : outgoingEdgesOf(v);
                for (final MultiSampleEdge e : nextEdges) {
                    final MultiDeBruijnVertex w = backwards ? getEdgeSource(e) : getEdgeTarget(e);
                    if (visited.contains(w)) // avoid repetitive work.
                        continue;

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Examples of org.broadinstitute.gatk.utils.collections.CountSet.incAll()

            final MultiDeBruijnVertex nextVertex = backwards ? graph.getEdgeSource(e) : graph.getEdgeTarget(e);
            if (e.isRef())
                nextReferenceVertex = nextVertex;
            else {
                final CountSet pathSizesPlusOne = pathSizes.clone();
                pathSizesPlusOne.incAll(1);
                graph.calculateRejoins(nextVertex, expectedAlternativePathRejoins, anchoring.referenceWithinAnchorsMap.keySet(), pathSizesPlusOne, true, backwards);
            }
        }
        return nextReferenceVertex;
    }

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Examples of org.broadinstitute.gatk.utils.collections.CountSet.incAll()

            final MultiDeBruijnVertex nextVertex = backwards ? graph.getEdgeSource(e) : graph.getEdgeTarget(e);
            if (e.isRef())
                nextReferenceVertex = nextVertex;
            else {
                final CountSet pathSizesPlusOne = pathSizes.clone();
                pathSizesPlusOne.incAll(1);
                graph.calculateRejoins(nextVertex, expectedAlternativePathRejoins, anchoring.referenceWithinAnchorsMap.keySet(), pathSizesPlusOne, true, backwards);
            }
        }
        return nextReferenceVertex;
    }

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