Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ContactMatrix	29	77	39	0.3161764731.6%	Show methods

Class ContactMatrix

Class ContactMatrix	Line # 29	Total Statements 77	Complexity 39	TOTAL Coverage 0.3161764731.6%
ContactMatrix(boolean)   ContactMatrix(boolean)	3737	1.01	1.01	0.0 0.00%
addContact(int,int,float) : void   addContact(int,int,float) : void	4848	17.017	8.08	0.0 0.00%
checkBounds(float) : void   checkBounds(float) : void	8686	4.04	3.03	0.0 0.00%
getPosition() : int   getPosition() : int	110110	1.01	1.01	0.0 0.00%
getContactHeight() : int   getContactHeight() : int	116116	1.01	1.01	0.0 0.00%
getContactAt(int) : double   getContactAt(int) : double	123123	4.04	2.02	0.0 0.00%
getContactList(int) : ContactListI   getContactList(int) : ContactListI	9898	3.03	3.03	0.0 0.00%
getFloatElementAt(int,int) : Float   getFloatElementAt(int,int) : Float	137137	11.011	3.03	0.0 0.00%
getElementAt(int,int) : double   getElementAt(int,int) : double	163163	4.04	2.02	0.0 0.00%
getMin() : float   getMin() : float	174174	1.01	1.01	0.0 0.00%
getMax() : float   getMax() : float	180180	1.01	1.01	0.0 0.00%
getAnnotLabel() : String   getAnnotLabel() : String	186186	1.01	1.01	0.0 0.00%
getAnnotDescr() : String   getAnnotDescr() : String	192192	1.01	1.01	0.0 0.00%
contactToFloatString(ContactMatrixI) : String   contactToFloatString(ContactMatrixI) : String	198198	13.013	6.06	0.95652175 0.9565217595.7%
fromFloatStringToContacts(String,int,int) : float[][]   fromFloatStringToContacts(String,int,int) : float[][]	229229	14.014	5.05	0.8636364 0.863636486.4%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.31617647	jalview.project.Jalview2xmlTests.testMatrixToFloatsAndBackjalview.project.Jalview2xmlTests.testMatrixToFloatsAndBack	1PASS
	0.31617647	jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore	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.datamodel;
22
23		import java.util.ArrayList;
24		import java.util.List;
25		import java.util.StringTokenizer;
26
27		import jalview.bin.Console;
28
		31.6% Uncovered Elements: 93 (136) Complexity: 39 Complexity Density: 0.51
29		public abstract class ContactMatrix extends GroupSetHolder
30		implements ContactMatrixI
31		{
32		/**
33		* are contacts reflexive ?
34		*/
35		boolean symmetric = true;
36
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
37	0	public ContactMatrix(boolean symmetric)...
38		{
39	0	this.symmetric = symmetric;
40		}
41
42		List<List<Float>> contacts = null;
43
44		int width = 0, numcontacts = 0;
45
46		float min = 0f, max = 0f;
47
		0% Uncovered Elements: 29 (29) Complexity: 8 Complexity Density: 0.47
48	0	public void addContact(int left, int right, float strength)...
49		{
50	0	if (left < 0 || right < 0)
51		{
52	0	throw new Error(new RuntimeException(
53		"Cannot have negative indices for contact left=" + left
54		+ " right=" + right + " strength=" + strength));
55		}
56	0	if (symmetric)
57		{
58	0	if (left > right)
59		{
60		// swap
61	0	int r = right;
62	0	right = left;
63	0	left = r;
64		}
65		}
66	0	if (contacts == null)
67		{
68		// TODO: use sparse list for efficiency ?
69	0	contacts = new ArrayList<List<Float>>();
70		}
71	0	List<Float> clist = contacts.get(left);
72	0	if (clist == null)
73		{
74	0	clist = new ArrayList<Float>();
75	0	contacts.set(left, clist);
76		}
77	0	Float last = clist.set(right, strength);
78		// TODO: if last is non null, may need to recompute range
79	0	checkBounds(strength);
80	0	if (last == null)
81		{
82	0	numcontacts++;
83		}
84		}
85
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
86	0	private void checkBounds(float strength)...
87		{
88	0	if (min > strength)
89		{
90	0	min = strength;
91		}
92	0	if (max < strength)
93		{
94	0	max = strength;
95		}
96		}
97
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
98	0	@Override...
99		public ContactListI getContactList(final int column)
100		{
101	0	if (column < 0 || column >= width)
102		{
103	0	return null;
104		}
105
106	0	return new ContactListImpl(new ContactListProviderI()
107		{
108		int p = column;
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public int getPosition()
112		{
113	0	return p;
114		}
115
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
116	0	@Override...
117		public int getContactHeight()
118		{
119	0	return width;
120
121		}
122
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
123	0	@Override...
124		public double getContactAt(int column)
125		{
126	0	Float cl = getFloatElementAt(column, p);
127	0	if (cl == null)
128		{
129		// return 0 not NaN ?
130	0	return Double.NaN;
131		}
132	0	return cl.doubleValue();
133		}
134		});
135		}
136
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27
137	0	private Float getFloatElementAt(int column, int p)...
138		{
139
140	0	List<Float> clist;
141	0	Float cl = null;
142	0	if (symmetric)
143		{
144	0	if (p < column)
145		{
146	0	clist = contacts.get(p);
147	0	cl = clist.get(column);
148		}
149		else
150		{
151	0	clist = contacts.get(column);
152	0	cl = clist.get(p);
153		}
154		}
155		else
156		{
157	0	clist = contacts.get(p);
158	0	cl = clist.get(column);
159		}
160	0	return cl;
161		}
162
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
163	0	@Override...
164		public double getElementAt(int column, int row)
165		{
166	0	Float cl = getFloatElementAt(column, row);
167	0	if (cl != null)
168		{
169	0	return cl;
170		}
171	0	throw (new RuntimeException("Out of Bounds " + column + "," + row));
172		}
173
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
174	0	@Override...
175		public float getMin()
176		{
177	0	return min;
178		}
179
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public float getMax()
182		{
183	0	return max;
184		}
185
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
186	0	@Override...
187		public String getAnnotLabel()
188		{
189	0	return "Contact Matrix";
190		}
191
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	@Override...
193		public String getAnnotDescr()
194		{
195	0	return "Contact Matrix";
196		}
197
		95.7% Uncovered Elements: 1 (23) Complexity: 6 Complexity Density: 0.46
198	5	public static String contactToFloatString(ContactMatrixI cm)...
199		{
200	5	StringBuilder sb = new StringBuilder();
201	2049	for (int c = 0; c < cm.getWidth(); c++)
202		{
203	2044	ContactListI cl = cm.getContactList(c);
204	2044	long lastsb = -1;
205	2044	if (cl != null)
206		{
207	4002528	for (int h = 0; h <= cl.getContactHeight(); h++)
208		{
209	4000484	if (sb.length() > 0)
210		{
211	4000479	if (sb.length() - lastsb > 320)
212		{
213		// newline
214	56466	sb.append('\n');
215	56466	lastsb = sb.length();
216		}
217		else
218		{
219	3944013	sb.append('\t');
220		}
221		}
222	4000484	sb.append(cl.getContactAt(h));
223		}
224		}
225		}
226	5	return sb.toString();
227		}
228
		86.4% Uncovered Elements: 3 (22) Complexity: 5 Complexity Density: 0.36
229	4	public static float[][] fromFloatStringToContacts(String values, int cols,...
230		int rows)
231		{
232	4	float[][] vals = new float[cols][rows];
233	4	StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
234	4	int c = 0, r = 0;
235	4000363	while (tabsep.hasMoreTokens())
236		{
237	4000363	double elem = Double.valueOf(tabsep.nextToken());
238	4000363	vals[c][r++] = (float) elem;
239	4000363	if (r >= vals[c].length)
240		{
241	2033	r = 0;
242	2033	c++;
243		}
244	4000363	if (c >= vals.length)
245		{
246	4	break;
247		}
248		}
249	4	if (tabsep.hasMoreElements())
250		{
251	0	Console.warn(
252		"Ignoring additional elements for Float string to contact matrix parsing.");
253		}
254	4	return vals;
255		}
256		}