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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.datamodel

File BinaryNode.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

16
56
24
1
383
167
37
0.66
2.33
24
1.54

Classes

Class Line # Actions
BinaryNode 31 56 37
0.62562.5%
 

Contributing tests

This file is covered by 14 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.datamodel;
22   
23    import java.awt.Color;
24   
25    /**
26    * Represent a node in a binary tree
27    *
28    * @author $mclamp (probably!)$
29    * @version $Revision$
30    */
 
31    public class BinaryNode<T>
32    {
33    T element;
34   
35    String name;
36   
37    BinaryNode<T> left;
38   
39    BinaryNode<T> right;
40   
41    BinaryNode<T> parent;
42   
43    /** Bootstrap value */
44    public int bootstrap;
45   
46    /** DOCUMENT ME!! */
47    public double dist;
48   
49    /** DOCUMENT ME!! */
50    public int count;
51   
52    /** DOCUMENT ME!! */
53    public double height;
54   
55    /** DOCUMENT ME!! */
56    public float ycount;
57   
58    /** DOCUMENT ME!! */
59    public Color color = Color.black;
60   
61    /**
62    * if true, node is created to simulate polytomy between parent and its 3 or
63    * more children
64    */
65    public boolean dummy = false;
66   
67    /**
68    * Creates a new BinaryNode object.
69    */
 
70  563 toggle public BinaryNode()
71    {
72  563 left = right = parent = null;
73  563 bootstrap = 0;
74  563 dist = 0;
75    }
76   
77    /**
78    * Creates a new BinaryNode object.
79    *
80    * @param element
81    * DOCUMENT ME!
82    * @param parent
83    * DOCUMENT ME!
84    * @param name
85    * DOCUMENT ME!
86    */
 
87  396 toggle public BinaryNode(T element, BinaryNode<T> parent, String name,
88    double dist)
89    {
90  396 this();
91  396 this.element = element;
92  396 this.parent = parent;
93  396 this.name = name;
94  396 this.dist = dist;
95    }
96   
 
97  396 toggle public BinaryNode(T element, BinaryNode<T> parent, String name,
98    double dist, int bootstrap)
99    {
100  396 this(element, parent, name, dist);
101  396 this.bootstrap = bootstrap;
102    }
103   
 
104  396 toggle public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
105    int bootstrap, boolean dummy)
106    {
107  396 this(val, parent, name, dist, bootstrap);
108  396 this.dummy = dummy;
109    }
110   
111    /**
112    * DOCUMENT ME!
113    *
114    * @return DOCUMENT ME!
115    */
 
116  306 toggle public T element()
117    {
118  306 return element;
119    }
120   
121    /**
122    * DOCUMENT ME!
123    *
124    * @param v
125    * DOCUMENT ME!
126    *
127    * @return DOCUMENT ME!
128    */
 
129  283 toggle public T setElement(T v)
130    {
131  283 return element = v;
132    }
133   
134    /**
135    * DOCUMENT ME!
136    *
137    * @return DOCUMENT ME!
138    */
 
139  5487 toggle public BinaryNode<T> left()
140    {
141  5487 return left;
142    }
143   
144    /**
145    * DOCUMENT ME!
146    *
147    * @param n
148    * DOCUMENT ME!
149    *
150    * @return DOCUMENT ME!
151    */
 
152  260 toggle public BinaryNode<T> setLeft(BinaryNode<T> n)
153    {
154  260 return left = n;
155    }
156   
157    /**
158    * DOCUMENT ME!
159    *
160    * @return DOCUMENT ME!
161    */
 
162  3785 toggle public BinaryNode<T> right()
163    {
164  3785 return right;
165    }
166   
167    /**
168    * DOCUMENT ME!
169    *
170    * @param n
171    * DOCUMENT ME!
172    *
173    * @return DOCUMENT ME!
174    */
 
175  280 toggle public BinaryNode<T> setRight(BinaryNode<T> n)
176    {
177  280 return right = n;
178    }
179   
180    /**
181    * DOCUMENT ME!
182    *
183    * @return DOCUMENT ME!
184    */
 
185  2120 toggle public BinaryNode<T> parent()
186    {
187  2120 return parent;
188    }
189   
190    /**
191    * DOCUMENT ME!
192    *
193    * @param n
194    * DOCUMENT ME!
195    *
196    * @return DOCUMENT ME!
197    */
 
198  144 toggle public BinaryNode<T> setParent(BinaryNode<T> n)
199    {
200  144 return parent = n;
201    }
202   
203    /**
204    * DOCUMENT ME!
205    *
206    * @return DOCUMENT ME!
207    */
 
208  278 toggle public boolean isLeaf()
209    {
210  278 return (left == null) && (right == null);
211    }
212   
213    /**
214    * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of
215    * this node (removing any old references) a null parameter DOES NOT mean that
216    * the pointer to the corresponding child node is set to NULL - you should use
217    * setChild(null), or detach() for this.
218    *
219    */
 
220  0 toggle public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)
221    {
222  0 if (leftchild != null)
223    {
224  0 this.setLeft(leftchild);
225  0 leftchild.detach();
226  0 leftchild.setParent(this);
227    }
228   
229  0 if (rightchild != null)
230    {
231  0 this.setRight(rightchild);
232  0 rightchild.detach();
233  0 rightchild.setParent(this);
234    }
235    }
236   
237    /**
238    * Detaches the node from the binary tree, along with all its child nodes.
239    *
240    * @return BinaryNode The detached node.
241    */
 
242  20 toggle public BinaryNode<T> detach()
243    {
244  20 if (this.parent != null)
245    {
246  20 if (this.parent.left == this)
247    {
248  0 this.parent.left = null;
249    }
250    else
251    {
252  20 if (this.parent.right == this)
253    {
254  20 this.parent.right = null;
255    }
256    }
257    }
258   
259  20 this.parent = null;
260   
261  20 return this;
262    }
263   
264    /**
265    * Traverses up through the tree until a node with a free leftchild is
266    * discovered.
267    *
268    * @return BinaryNode
269    */
 
270  0 toggle public BinaryNode<T> ascendLeft()
271    {
272  0 BinaryNode<T> c = this;
273   
274  0 do
275    {
276  0 c = c.parent();
277  0 } while ((c != null) && (c.left() != null) && !c.left().isLeaf());
278   
279  0 return c;
280    }
281   
282    /**
283    * Traverses up through the tree until a node with a free rightchild is
284    * discovered. Jalview builds trees by descent on the left, so this may be
285    * unused.
286    *
287    * @return BinaryNode
288    */
 
289  0 toggle public BinaryNode<T> ascendRight()
290    {
291  0 BinaryNode<T> c = this;
292   
293  0 do
294    {
295  0 c = c.parent();
296  0 } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
297   
298  0 return c;
299    }
300   
301    /**
302    *
303    * set the display name
304    *
305    * @param new
306    * name
307    */
 
308  263 toggle public void setName(String name)
309    {
310  263 this.name = name;
311    }
312   
313    /**
314    *
315    *
316    * @return the display name for this node
317    */
 
318  802 toggle public String getName()
319    {
320  802 return this.name;
321    }
322   
323    /**
324    * set integer bootstrap value
325    *
326    * @param boot
327    */
 
328  188 toggle public void setBootstrap(int boot)
329    {
330  188 this.bootstrap = boot;
331    }
332   
333    /**
334    * get bootstrap
335    *
336    * @return integer value
337    */
 
338  234 toggle public int getBootstrap()
339    {
340  234 return bootstrap;
341    }
342   
343    /**
344    * @param dummy
345    * true if node is created for the representation of polytomous trees
346    */
 
347  134 toggle public boolean isDummy()
348    {
349  134 return dummy;
350    }
351   
352    /**
353    * DOCUMENT ME!
354    *
355    * @param newstate
356    * DOCUMENT ME!
357    *
358    * @return DOCUMENT ME!
359    */
 
360  0 toggle public boolean setDummy(boolean newstate)
361    {
362  0 boolean oldstate = dummy;
363  0 dummy = newstate;
364   
365  0 return oldstate;
366    }
367   
368    /**
369    * ascends the tree but doesn't stop until a non-dummy node is discovered.
370    *
371    */
 
372  188 toggle public BinaryNode<T> AscendTree()
373    {
374  188 BinaryNode<T> c = this;
375   
376  188 do
377    {
378  188 c = c.parent();
379  188 } while ((c != null) && c.dummy);
380   
381  188 return c;
382    }
383    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.