Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TreeEngine	30	71	26	0.7428571674.3%	Show methods

Class TreeEngine

Class TreeEngine	Line # 30	Total Statements 71	Complexity 26	TOTAL Coverage 0.7428571674.3%
findr(int,int) : double   findr(int,int) : double	7171	7.07	6.06	1.0 1.0100%
joinClusters(int,int) : void   joinClusters(int,int) : void	9797	16.016	1.01	1.0 1.0100%
findMaxDist(BinaryNode) : void   findMaxDist(BinaryNode) : void	149149	9.09	5.05	0.8666667 0.866666786.7%
cluster() : void   cluster() : void	177177	11.011	2.02	1.0 1.0100%
_reCount(BinaryNode) : void   _reCount(BinaryNode) : void	213213	11.011	4.04	0.8666667 0.866666786.7%
findHeight(BinaryNode) : double   findHeight(BinaryNode) : double	255255	14.014	6.06	0.0 0.00%
reCount(BinaryNode) : void   reCount(BinaryNode) : void	300300	2.02	1.01	1.0 1.0100%
getTopNode() : BinaryNode   getTopNode() : BinaryNode	313313	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.74285716	jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore	1PASS
	0.74285716	jalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrixjalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrix	1PASS
	0.74285716	jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine	1PASS

 

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.analysis;
22
23		import java.util.BitSet;
24		import java.util.Vector;
25
26		import jalview.datamodel.BinaryNode;
27		import jalview.datamodel.SequenceNode;
28		import jalview.math.MatrixI;
29
		74.3% Uncovered Elements: 27 (105) Complexity: 26 Complexity Density: 0.37
30		public abstract class TreeEngine
31		{
32
33		protected Vector<BitSet> clusters;
34
35		protected BitSet done;
36
37		protected int noseqs;
38
39		protected int noClus;
40
41		protected MatrixI distances;
42
43		protected double ri;
44
45		protected double rj;
46
47		protected Vector<BinaryNode> node;
48
49		BinaryNode maxdist;
50
51		double maxDistValue;
52
53		protected int mini;
54
55		protected int minj;
56
57		protected BinaryNode top;
58
59		protected int ycount;
60
61		double maxheight;
62
63		/**
64		* Calculates and returns r, whatever that is
65		*
66		* @param i
67		* @param j
68		*
69		* @return
70		*/
		100% Uncovered Elements: 0 (13) Complexity: 6 Complexity Density: 0.86
71	144	protected double findr(int i, int j)...
72		{
73	144	double tmp = 1;
74
75	7248	for (int k = 0; k < noseqs; k++)
76		{
77	7104	if ((k != i) && (k != j) && (!done.get(k)))
78		{
79	3408	tmp = tmp + distances.getValue(i, k);
80		}
81		}
82
83	144	if (noClus > 2)
84		{
85	138	tmp = tmp / (noClus - 2);
86		}
87
88	144	return tmp;
89		}
90
91		/**
92		* Merges cluster(j) to cluster(i) and recalculates cluster and node distances
93		*
94		* @param i
95		* @param j
96		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06
97	72	protected void joinClusters(final int i, final int j)...
98		{
99	72	double dist = distances.getValue(i, j);
100
101	72	ri = findr(i, j);
102	72	rj = findr(j, i);
103
104	72	findClusterDistance(i, j);
105
106	72	BinaryNode sn = new BinaryNode();
107
108	72	sn.setLeft((node.elementAt(i)));
109	72	sn.setRight((node.elementAt(j)));
110
111	72	BinaryNode tmpi = (node.elementAt(i));
112	72	BinaryNode tmpj = (node.elementAt(j));
113
114	72	findNewDistances(tmpi, tmpj, dist);
115
116	72	tmpi.setParent(sn);
117	72	tmpj.setParent(sn);
118
119	72	node.setElementAt(sn, i);
120
121		/*
122		* move the members of cluster(j) to cluster(i)
123		* and mark cluster j as out of the game
124		*/
125	72	clusters.get(i).or(clusters.get(j));
126	72	clusters.get(j).clear();
127	72	done.set(j);
128		}
129
130		protected abstract void findNewDistances(BinaryNode nodei,
131		BinaryNode nodej, double previousDistance);
132
133		/**
134		* Calculates and saves the distance between the combination of cluster(i) and
135		* cluster(j) and all other clusters. The form of the calculation depends on
136		* the tree clustering method being used.
137		*
138		* @param i
139		* @param j
140		*/
141		protected abstract void findClusterDistance(int i, int j);
142
143		/**
144		* Finds the node, at or below the given node, with the maximum distance, and
145		* saves the node and the distance value
146		*
147		* @param nd
148		*/
		86.7% Uncovered Elements: 2 (15) Complexity: 5 Complexity Density: 0.56
149	147	protected void findMaxDist(BinaryNode nd)...
150		{
151	147	if (nd == null)
152		{
153	0	return;
154		}
155
156	147	if ((nd.left() == null) && (nd.right() == null))
157		{
158	75	double dist = nd.dist;
159
160	75	if (dist > maxDistValue)
161		{
162	12	maxdist = nd;
163	12	maxDistValue = dist;
164		}
165		}
166		else
167		{
168	72	findMaxDist((BinaryNode) nd.left());
169	72	findMaxDist((BinaryNode) nd.right());
170		}
171		}
172
173		/**
174		* Form clusters by grouping sub-clusters, starting from one sequence per
175		* cluster, and finishing when only two clusters remain
176		*/
		100% Uncovered Elements: 0 (13) Complexity: 2 Complexity Density: 0.18
177	3	protected void cluster()...
178		{
179	72	while (noClus > 2)
180		{
181	69	findMinDistance();
182
183	69	joinClusters(mini, minj);
184
185	69	noClus--;
186		}
187
188	3	int rightChild = done.nextClearBit(0);
189	3	int leftChild = done.nextClearBit(rightChild + 1);
190
191	3	joinClusters(leftChild, rightChild);
192	3	top = (node.elementAt(leftChild));
193
194	3	reCount(top);
195	3	findHeight(top);
196	3	findMaxDist(top);
197		}
198
199		/**
200		* Returns the minimum distance between two clusters, and also sets the
201		* indices of the clusters in fields mini and minj
202		*
203		* @return
204		*/
205		protected abstract double findMinDistance();
206
207		/**
208		* DOCUMENT ME!
209		*
210		* @param nd
211		* DOCUMENT ME!
212		*/
		86.7% Uncovered Elements: 2 (15) Complexity: 4 Complexity Density: 0.36
213	147	protected void _reCount(BinaryNode nd)...
214		{
215		// if (_lycount<_lylimit)
216		// {
217		// jalview.bin.Console.errPrintln("Warning: depth of _recount greater than
218		// number of
219		// nodes.");
220		// }
221	147	if (nd == null)
222		{
223	0	return;
224		}
225		// _lycount++;
226
227	147	if ((nd.left() != null) && (nd.right() != null))
228		{
229
230	72	_reCount(nd.left());
231	72	_reCount((BinaryNode) nd.right());
232
233	72	BinaryNode l = nd.left();
234	72	BinaryNode r = nd.right();
235
236	72	nd.count = l.count + r.count;
237	72	nd.ycount = (l.ycount + r.ycount) / 2;
238		}
239		else
240		{
241	75	nd.count = 1;
242	75	nd.ycount = ycount++;
243		}
244		// _lycount--;
245		}
246
247		/**
248		* DOCUMENT ME!
249		*
250		* @param nd
251		* DOCUMENT ME!
252		*
253		* @return DOCUMENT ME!
254		*/
		0% Uncovered Elements: 22 (22) Complexity: 6 Complexity Density: 0.43
255	0	double findHeight(BinaryNode nd)...
256		{
257	0	if (nd == null)
258		{
259	0	return maxheight;
260		}
261
262	0	if ((nd.left() == null) && (nd.right() == null))
263		{
264	0	nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
265
266	0	if (nd.height > maxheight)
267		{
268	0	return nd.height;
269		}
270		else
271		{
272	0	return maxheight;
273		}
274		}
275		else
276		{
277	0	if (nd.parent() != null)
278		{
279	0	nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
280		}
281		else
282		{
283	0	maxheight = 0;
284	0	nd.height = (float) 0.0;
285		}
286
287	0	maxheight = findHeight((BinaryNode) (nd.left()));
288	0	maxheight = findHeight((BinaryNode) (nd.right()));
289		}
290
291	0	return maxheight;
292		}
293
294		/**
295		* DOCUMENT ME!
296		*
297		* @param nd
298		* DOCUMENT ME!
299		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
300	3	void reCount(BinaryNode nd)...
301		{
302	3	ycount = 0;
303		// _lycount = 0;
304		// _lylimit = this.node.size();
305	3	_reCount(nd);
306		}
307
308		/**
309		* DOCUMENT ME!
310		*
311		* @return DOCUMENT ME!
312		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
313	9	public BinaryNode getTopNode()...
314		{
315	9	return top;
316		}
317
318		}