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package jalview.datamodel; |
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import java.awt.Color; |
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@author |
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@version |
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| 46.9% |
Uncovered Elements: 77 (145) |
Complexity: 54 |
Complexity Density: 0.67 |
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public class BinaryNode<T> |
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{ |
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T element; |
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String name; |
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String label = null; |
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BinaryNode<T> left; |
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BinaryNode<T> right; |
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BinaryNode<T> parent; |
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public int bootstrap; |
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public double dist; |
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public int count; |
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public double height; |
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public float ycount; |
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public Color color = Color.black; |
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public boolean dummy = false; |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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public BinaryNode()... |
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{ |
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left = right = parent = null; |
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bootstrap = 0; |
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dist = 0; |
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} |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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public BinaryNode(T element, BinaryNode<T> parent, String name,... |
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double dist) |
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{ |
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this(); |
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this.element = element; |
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this.parent = parent; |
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this.name = name; |
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this.dist = dist; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public BinaryNode(T element, BinaryNode<T> parent, String name,... |
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double dist, int bootstrap) |
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{ |
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this(element, parent, name, dist); |
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this.bootstrap = bootstrap; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,... |
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int bootstrap, boolean dummy) |
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{ |
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this(val, parent, name, dist, bootstrap); |
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this.dummy = dummy; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public T element()... |
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{ |
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return element; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public T setElement(T v)... |
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{ |
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return element = v; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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5487 |
public BinaryNode<T> left()... |
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{ |
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5487 |
return left; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public BinaryNode<T> setLeft(BinaryNode<T> n)... |
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{ |
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return left = n; |
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} |
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160 |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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3785 |
public BinaryNode<T> right()... |
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{ |
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3785 |
return right; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public BinaryNode<T> setRight(BinaryNode<T> n)... |
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{ |
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return right = n; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2120 |
public BinaryNode<T> parent()... |
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{ |
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2120 |
return parent; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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144 |
public BinaryNode<T> setParent(BinaryNode<T> n)... |
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{ |
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return parent = n; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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278 |
public boolean isLeaf()... |
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{ |
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return (left == null) && (right == null); |
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} |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
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public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)... |
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{ |
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if (leftchild != null) |
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{ |
226 |
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this.setLeft(leftchild); |
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leftchild.detach(); |
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leftchild.setParent(this); |
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} |
230 |
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if (rightchild != null) |
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{ |
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this.setRight(rightchild); |
234 |
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rightchild.detach(); |
235 |
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rightchild.setParent(this); |
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} |
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} |
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239 |
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240 |
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@return |
243 |
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| 69.2% |
Uncovered Elements: 4 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
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244 |
20 |
public BinaryNode<T> detach()... |
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{ |
246 |
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if (this.parent != null) |
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{ |
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if (this.parent.left == this) |
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{ |
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this.parent.left = null; |
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} |
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else |
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{ |
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if (this.parent.right == this) |
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{ |
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this.parent.right = null; |
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} |
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} |
259 |
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} |
260 |
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261 |
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this.parent = null; |
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return this; |
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} |
265 |
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267 |
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268 |
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269 |
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@return |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 4 |
Complexity Density: 1 |
|
272 |
0 |
public BinaryNode<T> ascendLeft()... |
273 |
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{ |
274 |
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BinaryNode<T> c = this; |
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276 |
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do |
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{ |
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c = c.parent(); |
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} while ((c != null) && (c.left() != null) && !c.left().isLeaf()); |
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281 |
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return c; |
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} |
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284 |
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286 |
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287 |
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288 |
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289 |
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@return |
290 |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 4 |
Complexity Density: 1 |
|
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0 |
public BinaryNode<T> ascendRight()... |
292 |
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{ |
293 |
0 |
BinaryNode<T> c = this; |
294 |
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|
295 |
0 |
do |
296 |
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{ |
297 |
0 |
c = c.parent(); |
298 |
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} while ((c != null) && (c.right() != null) && !c.right().isLeaf()); |
299 |
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300 |
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return c; |
301 |
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} |
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303 |
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304 |
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305 |
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306 |
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307 |
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@param |
308 |
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309 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
310 |
263 |
public void setName(String name)... |
311 |
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{ |
312 |
263 |
this.name = name; |
313 |
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} |
314 |
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315 |
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316 |
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317 |
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318 |
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@return |
319 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
320 |
802 |
public String getName()... |
321 |
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{ |
322 |
802 |
return this.name; |
323 |
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} |
324 |
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325 |
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326 |
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327 |
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328 |
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@param |
329 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
330 |
188 |
public void setBootstrap(int boot)... |
331 |
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{ |
332 |
188 |
this.bootstrap = boot; |
333 |
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} |
334 |
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335 |
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336 |
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337 |
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338 |
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@return |
339 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
340 |
234 |
public int getBootstrap()... |
341 |
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{ |
342 |
234 |
return bootstrap; |
343 |
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} |
344 |
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345 |
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346 |
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@param |
347 |
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|
348 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
349 |
134 |
public boolean isDummy()... |
350 |
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{ |
351 |
134 |
return dummy; |
352 |
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} |
353 |
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354 |
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355 |
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356 |
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357 |
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@param |
358 |
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359 |
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360 |
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@return |
361 |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
362 |
0 |
public boolean setDummy(boolean newstate)... |
363 |
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{ |
364 |
0 |
boolean oldstate = dummy; |
365 |
0 |
dummy = newstate; |
366 |
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|
367 |
0 |
return oldstate; |
368 |
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} |
369 |
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370 |
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|
371 |
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|
372 |
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|
373 |
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@return |
374 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
375 |
192 |
public boolean hasLabel()... |
376 |
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{ |
377 |
192 |
return label != null && !label.isEmpty(); |
378 |
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} |
379 |
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
380 |
0 |
public String getLabel()... |
381 |
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{ |
382 |
0 |
return label; |
383 |
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} |
384 |
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|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
385 |
0 |
public void setLabel(String label)... |
386 |
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{ |
387 |
0 |
this.label = label; |
388 |
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} |
389 |
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|
390 |
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|
391 |
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|
392 |
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|
393 |
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| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
394 |
188 |
public BinaryNode<T> AscendTree()... |
395 |
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{ |
396 |
188 |
BinaryNode<T> c = this; |
397 |
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|
398 |
188 |
do |
399 |
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{ |
400 |
188 |
c = c.parent(); |
401 |
188 |
} while ((c != null) && c.dummy); |
402 |
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|
403 |
188 |
return c; |
404 |
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} |
405 |
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|
|
|
| 45.5% |
Uncovered Elements: 6 (11) |
Complexity: 5 |
Complexity Density: 1 |
|
406 |
192 |
public String getDisplayName()... |
407 |
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{ |
408 |
192 |
if (name != null && !name.isBlank()) |
409 |
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{ |
410 |
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|
411 |
192 |
if (hasLabel()) |
412 |
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{ |
413 |
0 |
return getName() + "|" + label; |
414 |
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} |
415 |
192 |
return name; |
416 |
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} |
417 |
0 |
return hasLabel() ? label : ""; |
418 |
|
} |
419 |
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420 |
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421 |
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private String branchIdentifier = null; |
422 |
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|
423 |
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|
424 |
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|
425 |
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|
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
426 |
0 |
public String getBranchIdentifier()... |
427 |
|
{ |
428 |
0 |
if (branchIdentifier == null) |
429 |
|
{ |
430 |
0 |
setBranchIdentifier(true); |
431 |
|
} |
432 |
0 |
return branchIdentifier; |
433 |
|
} |
434 |
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|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 7 |
Complexity Density: 0.5 |
|
435 |
0 |
protected void setBranchIdentifier(boolean force)... |
436 |
|
{ |
437 |
|
|
438 |
0 |
if (branchIdentifier == null && !force) |
439 |
|
{ |
440 |
0 |
return; |
441 |
|
} |
442 |
0 |
StringBuilder sb = new StringBuilder(); |
443 |
0 |
if (getName() != null) |
444 |
|
{ |
445 |
0 |
sb.append(getName()); |
446 |
|
} |
447 |
0 |
if (left() != null) |
448 |
|
{ |
449 |
0 |
sb.append("::L:"); |
450 |
0 |
sb.append(left().getBranchIdentifier()); |
451 |
|
} |
452 |
0 |
if (right() != null) |
453 |
|
{ |
454 |
0 |
sb.append("::R:"); |
455 |
0 |
sb.append(right().getBranchIdentifier()); |
456 |
|
} |
457 |
0 |
branchIdentifier = sb.toString(); |
458 |
|
|
459 |
0 |
if (parent() != null) |
460 |
|
{ |
461 |
0 |
parent.setBranchIdentifier(false); |
462 |
|
} |
463 |
|
} |
464 |
|
} |