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package jalview.datamodel.features; |
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import jalview.datamodel.ContiguousI; |
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import jalview.datamodel.Range; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.List; |
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| 99.2% |
Uncovered Elements: 2 (242) |
Complexity: 62 |
Complexity Density: 0.41 |
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public class NCList<T extends ContiguousI> |
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{ |
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private int size; |
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private List<NCNode<T>> subranges; |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public NCList(List<T> ranges)... |
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{ |
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this(); |
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build(ranges); |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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protected void build(List<T> ranges)... |
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{ |
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Collections.sort(ranges, RangeComparator.BY_START_POSITION); |
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List<Range> sublists = buildSubranges(ranges); |
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for (Range sublist : sublists) |
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{ |
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subranges.add(new NCNode<T>(ranges.subList(sublist.start, |
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sublist.end + 1))); |
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} |
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size = ranges.size(); |
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} |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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public NCList(T entry)... |
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{ |
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this(); |
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subranges.add(new NCNode<>(entry)); |
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size = 1; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public NCList()... |
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{ |
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subranges = new ArrayList<NCNode<T>>(); |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (21) |
Complexity: 5 |
Complexity Density: 0.33 |
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protected List<Range> buildSubranges(List<T> ranges)... |
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{ |
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List<Range> sublists = new ArrayList<>(); |
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if (ranges.isEmpty()) |
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{ |
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return sublists; |
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} |
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int listStartIndex = 0; |
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long lastEndPos = Long.MAX_VALUE; |
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for (int i = 0; i < ranges.size(); i++) |
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{ |
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ContiguousI nextInterval = ranges.get(i); |
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long nextStart = nextInterval.getBegin(); |
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long nextEnd = nextInterval.getEnd(); |
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if (nextStart > lastEndPos || nextEnd > lastEndPos) |
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{ |
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sublists.add(new Range(listStartIndex, i - 1)); |
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listStartIndex = i; |
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} |
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lastEndPos = nextEnd; |
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} |
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sublists.add(new Range(listStartIndex, ranges.size() - 1)); |
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return sublists; |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void add(T entry)... |
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{ |
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add(entry, true); |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (58) |
Complexity: 15 |
Complexity Density: 0.39 |
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public synchronized boolean add(T entry, boolean allowDuplicates)... |
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{ |
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if (!allowDuplicates && contains(entry)) |
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{ |
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return false; |
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} |
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size++; |
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long start = entry.getBegin(); |
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long end = entry.getEnd(); |
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int candidateIndex = findFirstOverlap(start); |
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if (candidateIndex == -1) |
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{ |
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subranges.add(new NCNode<>(entry)); |
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return true; |
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} |
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boolean enclosing = false; |
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int firstEnclosed = 0; |
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int lastEnclosed = 0; |
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boolean overlapping = false; |
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for (int j = candidateIndex; j < subranges.size(); j++) |
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{ |
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NCNode<T> subrange = subranges.get(j); |
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if (end < subrange.getBegin() && !overlapping && !enclosing) |
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{ |
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subranges.add(j, new NCNode<>(entry)); |
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return true; |
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} |
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if (subrange.getBegin() <= start && subrange.getEnd() >= end) |
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{ |
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subrange.add(entry); |
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return true; |
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} |
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if (start <= subrange.getBegin()) |
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{ |
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if (end >= subrange.getEnd()) |
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{ |
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if (!enclosing) |
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{ |
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firstEnclosed = j; |
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} |
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lastEnclosed = j; |
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enclosing = true; |
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continue; |
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} |
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else |
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{ |
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if (enclosing) |
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{ |
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addEnclosingRange(entry, firstEnclosed, lastEnclosed); |
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return true; |
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} |
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else |
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{ |
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subranges.add(j, new NCNode<>(entry)); |
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return true; |
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} |
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} |
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} |
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else |
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{ |
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overlapping = true; |
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} |
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} |
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282 |
69 |
if (enclosing) |
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{ |
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addEnclosingRange(entry, firstEnclosed, lastEnclosed); |
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} |
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else |
287 |
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{ |
288 |
35 |
subranges.add(new NCNode<>(entry)); |
289 |
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} |
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291 |
69 |
return true; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 5 |
Complexity Density: 0.45 |
|
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21843 |
public boolean contains(T entry)... |
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{ |
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307 |
21843 |
int candidateIndex = findFirstOverlap(entry.getBegin()); |
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21843 |
if (candidateIndex == -1) |
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{ |
311 |
805 |
return false; |
312 |
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} |
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314 |
21038 |
int to = entry.getEnd(); |
315 |
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316 |
43921 |
for (int i = candidateIndex; i < subranges.size(); i++) |
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{ |
318 |
31176 |
NCNode<T> candidate = subranges.get(i); |
319 |
31176 |
if (candidate.getBegin() > to) |
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{ |
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324 |
547 |
break; |
325 |
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} |
326 |
30629 |
if (candidate.contains(entry)) |
327 |
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{ |
328 |
7746 |
return true; |
329 |
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} |
330 |
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} |
331 |
13292 |
return false; |
332 |
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} |
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336 |
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337 |
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338 |
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339 |
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@param |
340 |
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@param |
341 |
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@param |
342 |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
343 |
44 |
protected synchronized void addEnclosingRange(T entry, final int i,... |
344 |
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final int j) |
345 |
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{ |
346 |
44 |
NCList<T> newNCList = new NCList<>(); |
347 |
44 |
newNCList.addNodes(subranges.subList(i, j + 1)); |
348 |
44 |
NCNode<T> newNode = new NCNode<>(entry, newNCList); |
349 |
104 |
for (int k = j; k >= i; k--) |
350 |
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{ |
351 |
60 |
subranges.remove(k); |
352 |
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} |
353 |
44 |
subranges.add(i, newNode); |
354 |
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} |
355 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
356 |
44 |
protected void addNodes(List<NCNode<T>> nodes)... |
357 |
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{ |
358 |
44 |
for (NCNode<T> node : nodes) |
359 |
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{ |
360 |
60 |
subranges.add(node); |
361 |
60 |
size += node.size(); |
362 |
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} |
363 |
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} |
364 |
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365 |
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366 |
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367 |
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368 |
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369 |
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@param |
370 |
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371 |
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@param |
372 |
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373 |
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@return |
374 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
375 |
61 |
public List<T> findOverlaps(long from, long to)... |
376 |
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{ |
377 |
61 |
List<T> result = new ArrayList<>(); |
378 |
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|
379 |
61 |
findOverlaps(from, to, result); |
380 |
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381 |
61 |
return result; |
382 |
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} |
383 |
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384 |
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385 |
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386 |
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387 |
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388 |
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@param |
389 |
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@param |
390 |
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@param |
391 |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
392 |
765 |
protected void findOverlaps(long from, long to, List<T> result)... |
393 |
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{ |
394 |
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395 |
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396 |
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397 |
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|
398 |
765 |
int candidateIndex = findFirstOverlap(from); |
399 |
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|
400 |
765 |
if (candidateIndex == -1) |
401 |
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{ |
402 |
25 |
return; |
403 |
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} |
404 |
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|
405 |
1802 |
for (int i = candidateIndex; i < subranges.size(); i++) |
406 |
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{ |
407 |
1128 |
NCNode<T> candidate = subranges.get(i); |
408 |
1128 |
if (candidate.getBegin() > to) |
409 |
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{ |
410 |
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411 |
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412 |
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413 |
66 |
break; |
414 |
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} |
415 |
1062 |
candidate.findOverlaps(from, to, result); |
416 |
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} |
417 |
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418 |
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} |
419 |
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420 |
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421 |
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422 |
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423 |
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424 |
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425 |
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426 |
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@param |
427 |
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@return |
428 |
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| 90.9% |
Uncovered Elements: 1 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
429 |
23081 |
protected int findFirstOverlap(long from)... |
430 |
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{ |
431 |
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432 |
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433 |
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434 |
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435 |
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436 |
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437 |
23081 |
int i = 0; |
438 |
23081 |
if (subranges != null) |
439 |
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{ |
440 |
23081 |
for (NCNode<T> subrange : subranges) |
441 |
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{ |
442 |
24473 |
if (subrange.getEnd() >= from) |
443 |
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{ |
444 |
22232 |
return i; |
445 |
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} |
446 |
2241 |
i++; |
447 |
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} |
448 |
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} |
449 |
849 |
return -1; |
450 |
|
} |
451 |
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452 |
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453 |
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454 |
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455 |
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456 |
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457 |
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458 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
459 |
45 |
@Override... |
460 |
|
public String toString() |
461 |
|
{ |
462 |
45 |
return subranges.toString(); |
463 |
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} |
464 |
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465 |
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466 |
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|
467 |
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|
468 |
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|
469 |
|
@return |
470 |
|
|
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|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
471 |
2 |
public String prettyPrint()... |
472 |
|
{ |
473 |
2 |
StringBuilder sb = new StringBuilder(512); |
474 |
2 |
int offset = 0; |
475 |
2 |
int indent = 2; |
476 |
2 |
prettyPrint(sb, offset, indent); |
477 |
2 |
sb.append(System.lineSeparator()); |
478 |
2 |
return sb.toString(); |
479 |
|
} |
480 |
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|
481 |
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|
482 |
|
@param |
483 |
|
@param |
484 |
|
@param |
485 |
|
|
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|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
486 |
8 |
void prettyPrint(StringBuilder sb, int offset, int indent)... |
487 |
|
{ |
488 |
8 |
boolean first = true; |
489 |
8 |
for (NCNode<T> subrange : subranges) |
490 |
|
{ |
491 |
12 |
if (!first) |
492 |
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{ |
493 |
4 |
sb.append(System.lineSeparator()); |
494 |
|
} |
495 |
12 |
first = false; |
496 |
12 |
subrange.prettyPrint(sb, offset, indent); |
497 |
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} |
498 |
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} |
499 |
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|
500 |
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|
501 |
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|
502 |
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|
503 |
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|
504 |
|
@return |
505 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
506 |
223 |
public boolean isValid()... |
507 |
|
{ |
508 |
223 |
return isValid(Integer.MIN_VALUE, Integer.MAX_VALUE); |
509 |
|
} |
510 |
|
|
511 |
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512 |
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513 |
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514 |
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515 |
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516 |
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517 |
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|
518 |
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|
519 |
|
@param |
520 |
|
@param |
521 |
|
@return |
522 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
523 |
2776 |
boolean isValid(final int start, final int end)... |
524 |
|
{ |
525 |
2776 |
int lastStart = start; |
526 |
2776 |
for (NCNode<T> subrange : subranges) |
527 |
|
{ |
528 |
4538 |
if (subrange.getBegin() < lastStart) |
529 |
|
{ |
530 |
5 |
System.err.println("error in NCList: range " + subrange.toString() |
531 |
|
+ " starts before " + lastStart); |
532 |
5 |
return false; |
533 |
|
} |
534 |
4533 |
if (subrange.getEnd() > end) |
535 |
|
{ |
536 |
1 |
System.err.println("error in NCList: range " + subrange.toString() |
537 |
|
+ " ends after " + end); |
538 |
1 |
return false; |
539 |
|
} |
540 |
4532 |
lastStart = subrange.getBegin(); |
541 |
|
|
542 |
4532 |
if (!subrange.isValid()) |
543 |
|
{ |
544 |
7 |
return false; |
545 |
|
} |
546 |
|
} |
547 |
2763 |
return true; |
548 |
|
} |
549 |
|
|
550 |
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|
551 |
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|
552 |
|
|
553 |
|
@return |
554 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
555 |
1 |
public int getStart()... |
556 |
|
{ |
557 |
1 |
return subranges.isEmpty() ? 0 : subranges.get(0).getBegin(); |
558 |
|
} |
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
@return |
564 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
565 |
438 |
public int size()... |
566 |
|
{ |
567 |
438 |
return size; |
568 |
|
} |
569 |
|
|
570 |
|
|
571 |
|
|
572 |
|
|
573 |
|
@return |
574 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
575 |
330 |
public List<T> getEntries()... |
576 |
|
{ |
577 |
330 |
List<T> result = new ArrayList<>(); |
578 |
330 |
getEntries(result); |
579 |
330 |
return result; |
580 |
|
} |
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
@param |
586 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
587 |
523 |
void getEntries(List<T> result)... |
588 |
|
{ |
589 |
523 |
for (NCNode<T> subrange : subranges) |
590 |
|
{ |
591 |
613 |
subrange.getEntries(result); |
592 |
|
} |
593 |
|
} |
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
@param |
603 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 7 |
Complexity Density: 0.41 |
|
604 |
881 |
public synchronized boolean delete(T entry)... |
605 |
|
{ |
606 |
881 |
if (entry == null) |
607 |
|
{ |
608 |
1 |
return false; |
609 |
|
} |
610 |
1911 |
for (int i = 0; i < subranges.size(); i++) |
611 |
|
{ |
612 |
1344 |
NCNode<T> subrange = subranges.get(i); |
613 |
1344 |
NCList<T> subRegions = subrange.getSubRegions(); |
614 |
|
|
615 |
1344 |
if (subrange.getRegion() == entry) |
616 |
|
{ |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
|
622 |
|
|
623 |
|
|
624 |
|
|
625 |
124 |
subranges.remove(i); |
626 |
124 |
if (subRegions != null) |
627 |
|
{ |
628 |
60 |
subranges.addAll(subRegions.subranges); |
629 |
60 |
Collections.sort(subranges, RangeComparator.BY_START_POSITION); |
630 |
|
} |
631 |
124 |
size--; |
632 |
124 |
return true; |
633 |
|
} |
634 |
|
else |
635 |
|
{ |
636 |
1220 |
if (subRegions != null && subRegions.delete(entry)) |
637 |
|
{ |
638 |
189 |
size--; |
639 |
189 |
subrange.deleteSubRegionsIfEmpty(); |
640 |
189 |
return true; |
641 |
|
} |
642 |
|
} |
643 |
|
} |
644 |
567 |
return false; |
645 |
|
} |
646 |
|
} |