Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ContactMatrixI	31	50	35	0.00%	Show methods

Class ContactMatrixI

Class ContactMatrixI	Line # 31	Total Statements 50	Complexity 35	TOTAL Coverage 0.00%
hasGroupSet() : boolean   hasGroupSet() : boolean	6161	1.01	1.01	0.0 0.00%
hasGroups() : boolean   hasGroups() : boolean	6666	1.01	1.01	0.0 0.00%
getGroupsFor(int) : BitSet   getGroupsFor(int) : BitSet	7171	5.05	2.02	0.0 0.00%
getGroups() : List<BitSet>   getGroups() : List<BitSet>	8282	3.03	2.02	0.0 0.00%
hasTree() : boolean   hasTree() : boolean	9191	1.01	2.02	0.0 0.00%
getNewick() : String   getNewick() : String	101101	1.01	2.02	0.0 0.00%
getTreeMethod() : String   getTreeMethod() : String	106106	1.01	2.02	0.0 0.00%
hasCutHeight() : boolean   hasCutHeight() : boolean	111111	1.01	2.02	0.0 0.00%
getCutHeight() : double   getCutHeight() : double	116116	1.01	2.02	0.0 0.00%
updateGroups(List<BitSet>) : void   updateGroups(List<BitSet>) : void	121121	2.02	2.02	0.0 0.00%
setColorForGroup(BitSet,Color) : void   setColorForGroup(BitSet,Color) : void	129129	2.02	2.02	0.0 0.00%
getColourForGroup(BitSet) : Color   getColourForGroup(BitSet) : Color	137137	3.03	2.02	0.0 0.00%
randomlyReColourGroups() : void   randomlyReColourGroups() : void	151151	4.04	2.02	0.0 0.00%
transferGroupColorsTo(AlignmentAnnotation) : void   transferGroupColorsTo(AlignmentAnnotation) : void	163163	18.018	8.08	0.0 0.00%
getGroupColorForPosition(int) : Color   getGroupColorForPosition(int) : Color	211211	6.06	3.03	0.0 0.00%

 

Contributing 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.Arrays;
25		import java.util.BitSet;
26		import java.util.List;
27
28		import jalview.util.ColorUtils;
29		import jalview.ws.datamodel.MappableContactMatrixI;
30
		0% Uncovered Elements: 103 (103) Complexity: 35 Complexity Density: 0.7
31		public interface ContactMatrixI
32		{
33
34		ContactListI getContactList(int column);
35
36		float getMin();
37
38		float getMax();
39
40		String getAnnotDescr();
41
42		String getAnnotLabel();
43
44		/**
45		* string indicating how the contactMatrix should be rendered - stored in
46		* calcId
47		*
48		* @return
49		*/
50		String getType();
51
52		int getWidth();
53
54		int getHeight();
55
56		public GroupSetI getGroupSet();
57
58		/// proxy methods to simplify use of the interface
59		/// Mappable contact matrices can override these to perform mapping
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	default public boolean hasGroupSet()...
62		{
63	0	return getGroupSet() != null;
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	default boolean hasGroups()...
67		{
68	0	return hasGroupSet() && getGroupSet().hasGroups();
69		}
70
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
71	0	default BitSet getGroupsFor(int column)...
72		{
73	0	if (!hasGroupSet())
74		{
75	0	BitSet colbitset = new BitSet();
76	0	colbitset.set(column);
77	0	return colbitset;
78		}
79	0	return getGroupSet().getGroupsFor(column);
80		}
81
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
82	0	default List<BitSet> getGroups()...
83		{
84	0	if (!hasGroupSet())
85		{
86	0	return Arrays.asList();
87		}
88	0	return getGroupSet().getGroups();
89		}
90
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
91	0	default boolean hasTree()...
92		{
93	0	return hasGroupSet() ? getGroupSet().hasTree() : false;
94		}
95
96		/**
97		* Newick representation of clustered matrix
98		*
99		* @return null unless hasTree is true
100		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
101	0	default String getNewick()...
102		{
103	0	return hasGroupSet() ? getGroupSet().getNewick() : null;
104		}
105
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
106	0	default String getTreeMethod()...
107		{
108	0	return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
109		}
110
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
111	0	default boolean hasCutHeight()...
112		{
113	0	return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
114		}
115
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
116	0	default double getCutHeight()...
117		{
118	0	return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
119		}
120
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
121	0	default void updateGroups(List<BitSet> colGroups)...
122		{
123	0	if (hasGroupSet())
124		{
125	0	getGroupSet().updateGroups(colGroups);
126		}
127		}
128
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
129	0	default void setColorForGroup(BitSet bs, Color color)...
130		{
131	0	if (hasGroupSet())
132		{
133	0	getGroupSet().setColorForGroup(bs, color);
134		}
135		}
136
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
137	0	default Color getColourForGroup(BitSet bs)...
138		{
139	0	if (hasGroupSet())
140		{
141	0	return getGroupSet().getColourForGroup(bs);
142		}
143		else
144		{
145	0	return Color.white;
146		}
147		}
148
149		void setGroupSet(GroupSet makeGroups);
150
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
151	0	default void randomlyReColourGroups()...
152		{
153	0	if (hasGroupSet())
154		{
155	0	GroupSetI groups = getGroupSet();
156	0	for (BitSet group : groups.getGroups())
157		{
158	0	groups.setColorForGroup(group, ColorUtils.getARandomColor());
159		}
160		}
161		}
162
		0% Uncovered Elements: 30 (30) Complexity: 8 Complexity Density: 0.44
163	0	default void transferGroupColorsTo(AlignmentAnnotation aa)...
164		{
165	0	if (hasGroupSet())
166		{
167	0	GroupSetI groups = getGroupSet();
168		// stash colors in linked annotation row.
169		// doesn't work yet. TESTS!
170	0	int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
171		: 0;
172	0	Annotation ae;
173	0	Color gpcol = null;
174	0	int[] seqpos = null;
175	0	for (BitSet gp : groups.getGroups())
176		{
177	0	gpcol = groups.getColourForGroup(gp);
178	0	for (int p = gp.nextSetBit(0); p >= 0
179		&& p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
180		{
181	0	if (this instanceof MappableContactMatrixI)
182		{
183	0	MappableContactMatrixI mcm = (MappableContactMatrixI) this;
184	0	seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
185	0	if (seqpos == null)
186		{
187		// no mapping for this column.
188	0	continue;
189		}
190		// TODO: handle ranges...
191	0	ae = aa.getAnnotationForPosition(seqpos[0]);
192		}
193		else
194		{
195	0	ae = aa.getAnnotationForPosition(p + sstart);
196		}
197	0	if (ae != null)
198		{
199	0	ae.colour = gpcol.brighter().darker();
200		}
201		}
202		}
203		}
204		}
205
206		/**
207		* look up the colour for a column in the associated contact matrix
208		*
209		* @return Color.white or assigned colour
210		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
211	0	default Color getGroupColorForPosition(int column)...
212		{
213	0	if (hasGroupSet())
214		{
215	0	GroupSetI groups = getGroupSet();
216	0	for (BitSet gp : groups.getGroups())
217		{
218	0	if (gp.get(column))
219		{
220	0	return groups.getColourForGroup(gp);
221		}
222		}
223		}
224	0	return Color.white;
225		}
226
227		/**
228		* direct access to column and row position of matrix
229		*
230		* Implementations are allowed to throw RunTimeExceptions if _column/i are out
231		* of bounds
232		*
233		* @param column
234		* @param row
235		* @return
236		*/
237		double getElementAt(int column, int row);
238
239		}