Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Connectivity	34	22	7	0.00%	Show methods

Class Connectivity

Class Connectivity	Line # 34	Total Statements 22	Complexity 7	TOTAL Coverage 0.00%
getConnectivityForAlignmentView(AlignmentViewport,float[][],byte) : Hashtable<SequenceI, Integer>   getConnectivityForAlignmentView(AlignmentViewport,float[][],byte) : Hashtable<SequenceI, Integer>	3636	6.06	2.02	0.0 0.00%
getConnectivity(SequenceI[],float[][],byte) : Hashtable<SequenceI, Integer>   getConnectivity(SequenceI[],float[][],byte) : Hashtable<SequenceI, Integer>	6666	16.016	5.05	0.0 0.00%

 

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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.analysis;
22
23		import jalview.datamodel.SequenceI;
24		import jalview.gui.Desktop;
25		import jalview.gui.JvOptionPane;
26		import jalview.viewmodel.AlignmentViewport;
27
28		import java.util.Hashtable;
29
30		/**
31		* @Author MorellThomas
32		*/
33
		0% Uncovered Elements: 34 (34) Complexity: 7 Complexity Density: 0.32
34		public class Connectivity
35		{
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
36	0	public static Hashtable<SequenceI, Integer> getConnectivityForAlignmentView(...
37		AlignmentViewport av, float[][] scores, byte dim)
38		{
39	0	boolean isSelection = av.getSelectionGroup() != null
40		&& av.getSelectionGroup().getSize() > 0;
41	0	SequenceI[] sequences;
42	0	if (isSelection)
43		{
44	0	sequences = (SequenceI[]) av.getAlignmentView(isSelection)
45		.getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
46		}
47		else
48		{
49	0	sequences = av.getAlignment().getSequencesArray();
50		}
51
52	0	return Connectivity.getConnectivity(sequences, scores, dim);
53		}
54
55		/**
56		* Returns the number of unique connections for each sequence only connections
57		* with a score of above 0 count
58		*
59		* @param av
60		* sequences
61		* @param scores
62		* alignment scores
63		*
64		* @return connectivity
65		*/
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.31
66	0	public static Hashtable<SequenceI, Integer> getConnectivity(...
67		SequenceI[] sequences, float[][] scores, byte dim)
68		throws RuntimeException
69		{
70	0	Hashtable<SequenceI, Integer> connectivity = new Hashtable<SequenceI, Integer>();
71		// for each unique connection
72	0	for (int i = 0; i < sequences.length; i++)
73		{
74	0	connectivity.putIfAbsent(sequences[i], 0);
75	0	for (int j = 0; j < i; j++)
76		{
77	0	connectivity.putIfAbsent(sequences[j], 0);
78	0	int iOld = connectivity.get(sequences[i]);
79	0	int jOld = connectivity.get(sequences[j]);
80		// count the connection if its score is not NaN
81		// System.out.println(String.format("%s - %s : %f",
82		// sequences[i].getName(), sequences[j].getName(), scores[i][j]));
83	0	if (!Float.isNaN(scores[i][j]))
84		{
85	0	connectivity.put(sequences[i], ++iOld);
86	0	connectivity.put(sequences[j], ++jOld);
87		}
88		}
89		}
90
91		// if a sequence has too few connections, abort
92	0	connectivity.forEach((sequence, connection) -> {
93	0	System.out.println(
94		String.format("%s: %d", sequence.getName(), connection));
95	0	if (connection < dim)
96		{
97	0	JvOptionPane.showInternalMessageDialog(Desktop.desktop,
98		String.format(
99		"Insufficient number of connections for %s (%d, should be %d or more)",
100		sequence.getName(), connection, dim),
101		"Connectivity Error", JvOptionPane.WARNING_MESSAGE);
102	0	throw new ConnectivityException(sequence.getName(), connection,
103		dim);
104		}
105		});
106
107	0	return connectivity;
108		}
109
110		}