Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GroupSet	33	73	31	0.00%	Show methods

Class GroupSet

Class GroupSet	Line # 33	Total Statements 73	Complexity 31	TOTAL Coverage 0.00%
GroupSet(GroupSet)   GroupSet(GroupSet)	3737	6.06	1.01	0.0 0.00%
GroupSet()   GroupSet()	4747	0.00	1.01	-1.0 -1.0 -
GroupSet(boolean,float,List<BitSet>,String,String)   GroupSet(boolean,float,List<BitSet>,String,String)	5252	5.05	1.01	0.0 0.00%
hasGroups() : boolean   hasGroups() : boolean	6262	1.01	1.01	0.0 0.00%
getNewick() : String   getNewick() : String	7070	1.01	1.01	0.0 0.00%
hasTree() : boolean   hasTree() : boolean	7676	1.01	1.01	0.0 0.00%
updateGroups(List<BitSet>) : void   updateGroups(List<BitSet>) : void	8888	2.02	2.02	0.0 0.00%
getGroupsFor(int) : BitSet   getGroupsFor(int) : BitSet	9797	7.07	3.03	0.0 0.00%
getColourForGroup(BitSet) : Color   getColourForGroup(BitSet) : Color	118118	6.06	3.03	0.0 0.00%
setColorForGroup(BitSet,Color) : void   setColorForGroup(BitSet,Color) : void	133133	1.01	1.01	0.0 0.00%
restoreGroups(List<BitSet>,String,String,double) : void   restoreGroups(List<BitSet>,String,String,double) : void	139139	4.04	1.01	0.0 0.00%
hasCutHeight() : boolean   hasCutHeight() : boolean	150150	1.01	1.01	0.0 0.00%
getCutHeight() : double   getCutHeight() : double	156156	1.01	1.01	0.0 0.00%
getTreeMethod() : String   getTreeMethod() : String	162162	1.01	1.01	0.0 0.00%
makeGroups(ContactMatrixI,boolean) : GroupSet   makeGroups(ContactMatrixI,boolean) : GroupSet	168168	1.01	1.01	0.0 0.00%
makeGroups(ContactMatrixI,boolean,float,boolean) : GroupSet   makeGroups(ContactMatrixI,boolean,float,boolean) : GroupSet	173173	34.034	10.010	0.0 0.00%
getGroups() : List<BitSet>   getGroups() : List<BitSet>	237237	1.01	1.01	0.0 0.00%

 

Contributing tests

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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.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
		0% Uncovered Elements: 116 (116) Complexity: 31 Complexity Density: 0.42
33		public class GroupSet implements GroupSetI
34		{
35		List<BitSet> groups = Arrays.asList();
36
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
37	0	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
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
47	0	public GroupSet()...
48		{
49		// TODO Auto-generated constructor stub
50		}
51
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
52	0	public GroupSet(boolean abs2, float thresh2, List<BitSet> groups2,...
53		String treeType2, String newick2)
54		{
55	0	abs = abs2;
56	0	thresh = thresh2;
57	0	groups = groups2;
58	0	treeType = treeType2;
59	0	newick = newick2;
60		}
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	@Override...
63		public boolean hasGroups()
64		{
65	0	return groups != null;
66		}
67
68		String newick = null;
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	@Override...
71		public String getNewick()
72		{
73	0	return newick;
74		}
75
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	@Override...
77		public boolean hasTree()
78		{
79	0	return newick != null && newick.length() > 0;
80		}
81
82		boolean abs = false;
83
84		double thresh = 0;
85
86		String treeType = null;
87
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
88	0	@Override...
89		public void updateGroups(List<BitSet> colGroups)
90		{
91	0	if (colGroups != null)
92		{
93	0	groups = colGroups;
94		}
95		}
96
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
97	0	@Override...
98		public BitSet getGroupsFor(int column)
99		{
100	0	if (groups != null)
101		{
102	0	for (BitSet gp : groups)
103		{
104	0	if (gp.get(column))
105		{
106	0	return gp;
107		}
108		}
109		}
110		// return singleton set;
111	0	BitSet bs = new BitSet();
112	0	bs.set(column);
113	0	return bs;
114		}
115
116		HashMap<BitSet, Color> colorMap = new HashMap<>();
117
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
118	0	@Override...
119		public Color getColourForGroup(BitSet bs)
120		{
121	0	if (bs == null)
122		{
123	0	return Color.white;
124		}
125	0	Color groupCol = colorMap.get(bs);
126	0	if (groupCol == null)
127		{
128	0	return Color.white;
129		}
130	0	return groupCol;
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public void setColorForGroup(BitSet bs, Color color)
135		{
136	0	colorMap.put(bs, color);
137		}
138
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
139	0	@Override...
140		public void restoreGroups(List<BitSet> newgroups, String treeMethod,
141		String tree, double thresh2)
142		{
143	0	treeType = treeMethod;
144	0	groups = newgroups;
145	0	thresh = thresh2;
146	0	newick = tree;
147
148		}
149
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	@Override...
151		public boolean hasCutHeight()
152		{
153	0	return groups != null && thresh != 0;
154		}
155
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	@Override...
157		public double getCutHeight()
158		{
159	0	return thresh;
160		}
161
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
162	0	@Override...
163		public String getTreeMethod()
164		{
165	0	return treeType;
166		}
167
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
168	0	public static GroupSet makeGroups(ContactMatrixI matrix, boolean autoCut)...
169		{
170	0	return makeGroups(matrix, autoCut, 0, autoCut);
171		}
172
		0% Uncovered Elements: 50 (50) Complexity: 10 Complexity Density: 0.29
173	0	public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto,...
174		float thresh, boolean abs)
175		{
176	0	AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
177		matrix, true);
178	0	double height = clusterer.findHeight(clusterer.getTopNode());
179	0	Console.debug("Column tree height: " + height);
180	0	String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
181		true).print();
182	0	String treeType = "UPGMA";
183	0	Console.trace("Newick string\n" + newick);
184
185	0	List<BinaryNode> nodegroups;
186	0	float cut = -1f;
187	0	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	0	if (abs ? (height > thresh) : (0 < thresh && thresh < 1))
210		{
211	0	cut = abs ? thresh : (float) (thresh * height);
212	0	Console.debug("Threshold " + cut + " for height=" + height);
213	0	nodegroups = clusterer.groupNodes(cut);
214		}
215		else
216		{
217	0	nodegroups = new ArrayList<BinaryNode>();
218	0	nodegroups.add(clusterer.getTopNode());
219		}
220		}
221
222	0	List<BitSet> groups = new ArrayList<>();
223	0	for (BinaryNode root : nodegroups)
224		{
225	0	BitSet gpset = new BitSet();
226	0	for (BinaryNode leaf : clusterer.findLeaves(root))
227		{
228	0	gpset.set((Integer) leaf.element());
229		}
230	0	groups.add(gpset);
231		}
232	0	GroupSet grps = new GroupSet(abs, (cut == -1f) ? thresh : cut, groups,
233		treeType, newick);
234	0	return grps;
235		}
236
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
237	0	@Override...
238		public List<BitSet> getGroups()
239		{
240	0	return groups;
241		}
242		}