Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ContactListImpl	33	35	17	0.1016949110.2%	Show methods

Class ContactListImpl

Class ContactListImpl	Line # 33	Total Statements 35	Complexity 17	TOTAL Coverage 0.1016949110.2%
newContactList(ContactListProviderI) : ContactListI   newContactList(ContactListProviderI) : ContactListI	3737	1.01	1.01	0.0 0.00%
ContactListImpl(ContactListProviderI)   ContactListImpl(ContactListProviderI)	4242	1.01	1.01	1.0 1.0100%
getPosition() : int   getPosition() : int	4747	1.01	1.01	0.0 0.00%
getContactAt(int) : double   getContactAt(int) : double	5353	1.01	1.01	1.0 1.0100%
getContactHeight() : int   getContactHeight() : int	5959	1.01	1.01	0.0 0.00%
getRangeFor(int,int) : ContactRange   getRangeFor(int,int) : ContactRange	6565	28.028	10.010	0.0 0.00%
getMappedPositionsFor(int,int) : int[]   getMappedPositionsFor(int,int) : int[]	122122	1.01	1.01	1.0 1.0100%
getColourForGroup() : Color   getColourForGroup() : Color	128128	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.10169491	jalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrixjalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrix	1PASS
	0.06779661	jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine	1PASS
	0.033898305	jalview.datamodel.ContactMatrixTest.testminMaxCalcjalview.datamodel.ContactMatrixTest.testminMaxCalc	1PASS
	0.033898305	jalview.datamodel.PAEContactMatrixTest.testMappableContactMatrixjalview.datamodel.PAEContactMatrixTest.testMappableContactMatrix	1PASS
	0.033898305	jalview.analysis.AlignmentUtilsTests.testAddReferenceContactMapjalview.analysis.AlignmentUtilsTests.testAddReferenceContactMap	1PASS
	0.033898305	jalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatricesjalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatrices	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.awt.Color;
24
25		import jalview.renderer.ContactGeometry.contactInterval;
26
27		/**
28		* helper class to compute min/max/mean for a range on a contact list
29		*
30		* @author jprocter
31		*
32		*/
		10.2% Uncovered Elements: 53 (59) Complexity: 17 Complexity Density: 0.49
33		public class ContactListImpl implements ContactListI
34		{
35		ContactListProviderI clist;
36
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
37	0	public static ContactListI newContactList(ContactListProviderI list)...
38		{
39	0	return new ContactListImpl(list);
40		}
41
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
42	1841	public ContactListImpl(ContactListProviderI list)...
43		{
44	1841	clist = list;
45		}
46
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	@Override...
48		public int getPosition()
49		{
50	0	return clist.getPosition();
51		}
52
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
53	208889	@Override...
54		public double getContactAt(int column)
55		{
56	208889	return clist.getContactAt(column);
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public int getContactHeight()
61		{
62	0	return clist.getContactHeight();
63		}
64
		0% Uncovered Elements: 44 (44) Complexity: 10 Complexity Density: 0.36
65	0	@Override...
66		public ContactRange getRangeFor(int from_column, int to_column)
67		{
68		// TODO: consider caching ContactRange for a particular call ?
69	0	if (clist instanceof ContactListI)
70		{
71		// clist may implement getRangeFor in a more efficient way, so use theirs
72	0	return ((ContactListI) clist).getRangeFor(from_column, to_column);
73		}
74	0	if (from_column < 0)
75		{
76	0	from_column = 0;
77		}
78	0	if (to_column >= getContactHeight())
79		{
80	0	to_column = getContactHeight() - 1;
81		}
82	0	ContactRange cr = new ContactRange();
83	0	cr.setFrom_column(from_column);
84	0	cr.setTo_column(to_column);
85	0	double tot = 0;
86	0	for (int i = from_column; i <= to_column; i++)
87		{
88	0	double contact = getContactAt(i);
89	0	tot += contact;
90	0	if (i == from_column)
91		{
92	0	cr.setMin(contact);
93	0	cr.setMax(contact);
94	0	cr.setMinPos(i);
95	0	cr.setMaxPos(i);
96		}
97		else
98		{
99	0	if (cr.getMax() < contact)
100		{
101	0	cr.setMax(contact);
102	0	cr.setMaxPos(i);
103		}
104	0	if (cr.getMin() < contact)
105		{
106	0	cr.setMin(contact);
107	0	cr.setMinPos(i);
108		}
109		}
110		}
111	0	if (tot > 0 && to_column > from_column)
112		{
113	0	cr.setMean(tot / (1 + to_column - from_column));
114		}
115		else
116		{
117	0	cr.setMean(tot);
118		}
119	0	return cr;
120		}
121
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
122	22	@Override...
123		public int[] getMappedPositionsFor(int cStart, int cEnd)
124		{
125	22	return clist.getMappedPositionsFor(cStart, cEnd);
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public Color getColourForGroup()
130		{
131	0	return clist.getColourForGroup();
132		}
133		}