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Coverage Report

  1. Project Clover database Mon Oct 6 2025 17:39:40 BST
  2. Package jalview.datamodel

File GroupSet.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
37% of files have more coverage

Code metrics

26
73
17
1
242
192
31
0.42
4.29
17
1.82

Classes

Class Line # Actions
GroupSet 33 73 31
0.5775862357.8%
 

Contributing tests

This file is covered by 49 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    import java.util.ArrayList;
25    import java.util.Arrays;
26    import java.util.BitSet;
27    import java.util.HashMap;
28    import java.util.List;
29   
30    import jalview.analysis.AverageDistanceEngine;
31    import jalview.bin.Console;
32   
 
33    public class GroupSet implements GroupSetI
34    {
35    List<BitSet> groups = Arrays.asList();
36   
 
37  0 toggle public GroupSet(GroupSet grps)
38    {
39  0 abs = grps.abs;
40  0 colorMap = new HashMap<BitSet, Color>(grps.colorMap);
41  0 groups = new ArrayList<BitSet>(grps.groups);
42  0 newick = grps.newick;
43  0 thresh = grps.thresh;
44  0 treeType = grps.treeType;
45    }
46   
 
47  149 toggle public GroupSet()
48    {
49    // TODO Auto-generated constructor stub
50    }
51   
 
52  2 toggle public GroupSet(boolean abs2, float thresh2, List<BitSet> groups2,
53    String treeType2, String newick2)
54    {
55  2 abs = abs2;
56  2 thresh = thresh2;
57  2 groups = groups2;
58  2 treeType = treeType2;
59  2 newick = newick2;
60    }
61   
 
62  14 toggle @Override
63    public boolean hasGroups()
64    {
65  14 return groups != null;
66    }
67   
68    String newick = null;
69   
 
70  6 toggle @Override
71    public String getNewick()
72    {
73  6 return newick;
74    }
75   
 
76  14 toggle @Override
77    public boolean hasTree()
78    {
79  14 return newick != null && newick.length() > 0;
80    }
81   
82    boolean abs = false;
83   
84    double thresh = 0;
85   
86    String treeType = null;
87   
 
88  0 toggle @Override
89    public void updateGroups(List<BitSet> colGroups)
90    {
91  0 if (colGroups != null)
92    {
93  0 groups = colGroups;
94    }
95    }
96   
 
97  4706 toggle @Override
98    public BitSet getGroupsFor(int column)
99    {
100  4706 if (groups != null)
101    {
102  4706 for (BitSet gp : groups)
103    {
104  0 if (gp.get(column))
105    {
106  0 return gp;
107    }
108    }
109    }
110    // return singleton set;
111  4706 BitSet bs = new BitSet();
112  4706 bs.set(column);
113  4706 return bs;
114    }
115   
116    HashMap<BitSet, Color> colorMap = new HashMap<>();
117   
 
118  4706 toggle @Override
119    public Color getColourForGroup(BitSet bs)
120    {
121  4706 if (bs == null)
122    {
123  0 return Color.white;
124    }
125  4706 Color groupCol = colorMap.get(bs);
126  4706 if (groupCol == null)
127    {
128  4706 return Color.white;
129    }
130  0 return groupCol;
131    }
132   
 
133  0 toggle @Override
134    public void setColorForGroup(BitSet bs, Color color)
135    {
136  0 colorMap.put(bs, color);
137    }
138   
 
139  20 toggle @Override
140    public void restoreGroups(List<BitSet> newgroups, String treeMethod,
141    String tree, double thresh2)
142    {
143  20 treeType = treeMethod;
144  20 groups = newgroups;
145  20 thresh = thresh2;
146  20 newick = tree;
147   
148    }
149   
 
150  12 toggle @Override
151    public boolean hasCutHeight()
152    {
153  12 return groups != null && thresh != 0;
154    }
155   
 
156  3 toggle @Override
157    public double getCutHeight()
158    {
159  3 return thresh;
160    }
161   
 
162  3 toggle @Override
163    public String getTreeMethod()
164    {
165  3 return treeType;
166    }
167   
 
168  0 toggle public static GroupSet makeGroups(ContactMatrixI matrix, boolean autoCut)
169    {
170  0 return makeGroups(matrix, autoCut, 0, autoCut);
171    }
172   
 
173  2 toggle public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto,
174    float thresh, boolean abs)
175    {
176  2 AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
177    matrix, true);
178  2 double height = clusterer.findHeight(clusterer.getTopNode());
179  2 Console.debug("Column tree height: " + height);
180  2 String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
181    true).print();
182  2 String treeType = "UPGMA";
183  2 Console.trace("Newick string\n" + newick);
184   
185  2 List<BinaryNode> nodegroups;
186  2 float cut = -1f;
187  2 if (auto)
188    {
189  0 double rootw = 0;
190  0 int p = 2;
191  0 BinaryNode bn = clusterer.getTopNode();
192  0 while (p-- > 0 & bn.left() != null)
193    {
194  0 if (bn.left() != null)
195    {
196  0 bn = bn.left();
197    }
198  0 if (bn.left() != null)
199    {
200  0 rootw = bn.height;
201    }
202    }
203  0 thresh = Math.max((float) (rootw / height) - 0.01f, 0);
204  0 cut = thresh;
205  0 nodegroups = clusterer.groupNodes(thresh);
206    }
207    else
208    {
209  2 if (abs ? (height > thresh) : (0 < thresh && thresh < 1))
210    {
211  2 cut = abs ? thresh : (float) (thresh * height);
212  2 Console.debug("Threshold " + cut + " for height=" + height);
213  2 nodegroups = clusterer.groupNodes(cut);
214    }
215    else
216    {
217  0 nodegroups = new ArrayList<BinaryNode>();
218  0 nodegroups.add(clusterer.getTopNode());
219    }
220    }
221   
222  2 List<BitSet> groups = new ArrayList<>();
223  2 for (BinaryNode root : nodegroups)
224    {
225  5 BitSet gpset = new BitSet();
226  5 for (BinaryNode leaf : clusterer.findLeaves(root))
227    {
228  16 gpset.set((Integer) leaf.element());
229    }
230  5 groups.add(gpset);
231    }
232  2 GroupSet grps = new GroupSet(abs, (cut == -1f) ? thresh : cut, groups,
233    treeType, newick);
234  2 return grps;
235    }
236   
 
237  15 toggle @Override
238    public List<BitSet> getGroups()
239    {
240  15 return groups;
241    }
242    }
  • Report generated by OpenClover v 4.4.1 on Mon Oct 6 2025 17:49:54 BST using coverage data from Mon Oct 6 2025 17:49:41 BST.
  • OpenClover is free and open-source software.