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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:38:20 GMT
  2. Package jalview.analysis

File AverageDistanceTree.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
54% of files have more coverage

Code metrics

18
32
4
1
141
79
15
0.47
8
4
3.75

Classes

Class Line # Actions
AverageDistanceTree 32 32 15
0.00%
 

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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 jalview.api.analysis.ScoreModelI;
24    import jalview.api.analysis.SimilarityParamsI;
25    import jalview.datamodel.BinaryNode;
26    import jalview.viewmodel.AlignmentViewport;
27   
28    /**
29    * This class implements distance calculations used in constructing a Average
30    * Distance tree (also known as UPGMA)
31    */
 
32    public class AverageDistanceTree extends TreeBuilder
33    {
34    /**
35    * Constructor
36    *
37    * @param av
38    * @param sm
39    * @param scoreParameters
40    */
 
41  0 toggle public AverageDistanceTree(AlignmentViewport av, ScoreModelI sm,
42    SimilarityParamsI scoreParameters)
43    {
44  0 super(av, sm, scoreParameters);
45    }
46   
47    /**
48    * Calculates and saves the distance between the combination of cluster(i) and
49    * cluster(j) and all other clusters. An average of the distances from
50    * cluster(i) and cluster(j) is calculated, weighted by the sizes of each
51    * cluster.
52    *
53    * @param i
54    * @param j
55    */
 
56  0 toggle @Override
57    protected void findClusterDistance(int i, int j)
58    {
59  0 int noi = clusters.elementAt(i).cardinality();
60  0 int noj = clusters.elementAt(j).cardinality();
61   
62    // New distances from cluster i to others
63  0 double[] newdist = new double[noseqs];
64   
65  0 for (int l = 0; l < noseqs; l++)
66    {
67  0 if ((l != i) && (l != j))
68    {
69  0 newdist[l] = ((distances.getValue(i, l) * noi)
70    + (distances.getValue(j, l) * noj)) / (noi + noj);
71    }
72    else
73    {
74  0 newdist[l] = 0;
75    }
76    }
77   
78  0 for (int ii = 0; ii < noseqs; ii++)
79    {
80  0 distances.setValue(i, ii, newdist[ii]);
81  0 distances.setValue(ii, i, newdist[ii]);
82    }
83    }
84   
85    /**
86    * {@inheritDoc}
87    */
 
88  0 toggle @Override
89    protected double findMinDistance()
90    {
91  0 double min = Double.MAX_VALUE;
92   
93  0 for (int i = 0; i < (noseqs - 1); i++)
94    {
95  0 for (int j = i + 1; j < noseqs; j++)
96    {
97  0 if (!done.get(i) && !done.get(j))
98    {
99  0 if (distances.getValue(i, j) < min)
100    {
101  0 mini = i;
102  0 minj = j;
103   
104  0 min = distances.getValue(i, j);
105    }
106    }
107    }
108    }
109  0 return min;
110    }
111   
112    /**
113    * {@inheritDoc}
114    */
 
115  0 toggle @Override
116    protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
117    double dist)
118    {
119  0 double ih = 0;
120  0 double jh = 0;
121   
122  0 BinaryNode sni = nodei;
123  0 BinaryNode snj = nodej;
124   
125  0 while (sni != null)
126    {
127  0 ih = ih + sni.dist;
128  0 sni = (BinaryNode) sni.left();
129    }
130   
131  0 while (snj != null)
132    {
133  0 jh = jh + snj.dist;
134  0 snj = (BinaryNode) snj.left();
135    }
136   
137  0 nodei.dist = ((dist / 2) - ih);
138  0 nodej.dist = ((dist / 2) - jh);
139    }
140   
141    }