Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UrlProviderImpl	39	26	12	0.00%	Show methods

Class UrlProviderImpl

Class UrlProviderImpl	Line # 39	Total Statements 26	Complexity 12	TOTAL Coverage 0.00%
getPrimaryUrl(String,HashMap<String, UrlLink>) : String   getPrimaryUrl(String,HashMap<String, UrlLink>) : String	4949	13.013	7.07	0.0 0.00%
getLinksForTable() : List<UrlLinkDisplay>   getLinksForTable() : List<UrlLinkDisplay>	8383	1.01	1.01	0.0 0.00%
getLinksForTable(HashMap<String, UrlLink>,ArrayList<String>,boolean) : ArrayList<UrlLinkDisplay>   getLinksForTable(HashMap<String, UrlLink>,ArrayList<String>,boolean) : ArrayList<UrlLinkDisplay>	8989	10.010	2.02	0.0 0.00%
isMiriamId(String) : boolean   isMiriamId(String) : boolean	113113	1.01	1.01	0.0 0.00%
isUserEntry(String) : boolean   isUserEntry(String) : boolean	118118	1.01	1.01	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.urls;
22
23		import jalview.urls.api.UrlProviderI;
24		import jalview.util.UrlLink;
25
26		import java.util.ArrayList;
27		import java.util.HashMap;
28		import java.util.List;
29		import java.util.Map.Entry;
30		import java.util.regex.Pattern;
31
32		/**
33		* Leaf node of UrlProvider composite
34		*
35		* @author $author$
36		* @version $Revision$
37		*/
38
		0% Uncovered Elements: 41 (41) Complexity: 12 Complexity Density: 0.46
39		public abstract class UrlProviderImpl implements UrlProviderI
40		{
41		// minimum length of substitution in url link string
42		protected static final int MIN_SUBST_LENGTH = 4;
43
44		private static final Pattern MIRIAM_PATTERN = Pattern
45		.compile("^MIR:\\d{8}$");
46
47		protected String primaryUrl;
48
		0% Uncovered Elements: 21 (21) Complexity: 7 Complexity Density: 0.54
49	0	protected String getPrimaryUrl(String seqid,...
50		HashMap<String, UrlLink> urls)
51		{
52	0	if (seqid.length() < MIN_SUBST_LENGTH)
53		{
54	0	return null;
55		}
56	0	else if (primaryUrl == null)
57		{
58	0	return null;
59		}
60	0	else if (!urls.containsKey(primaryUrl))
61		{
62	0	return null;
63		}
64		else
65		{
66	0	String url = null;
67	0	UrlLink urlLink = urls.get(primaryUrl);
68	0	String[] primaryUrls = urlLink.makeUrls(seqid, true);
69	0	if (primaryUrls == null || primaryUrls[0] == null
70		|| primaryUrls[0].length() < MIN_SUBST_LENGTH)
71		{
72	0	url = null;
73		}
74		else
75		{
76		// just take first URL made from regex
77	0	url = primaryUrls[1];
78		}
79	0	return url;
80		}
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public List<UrlLinkDisplay> getLinksForTable()
85		{
86	0	return null;
87		}
88
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
89	0	protected ArrayList<UrlLinkDisplay> getLinksForTable(...
90		HashMap<String, UrlLink> urls, ArrayList<String> selectedUrls,
91		boolean selected)
92		{
93	0	ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
94	0	for (Entry<String, UrlLink> entry : urls.entrySet())
95		{
96	0	String key = entry.getKey();
97	0	boolean isPrimary = (key.equals(primaryUrl));
98	0	boolean isSelected;
99	0	if (selectedUrls != null)
100		{
101	0	isSelected = selectedUrls.contains(key);
102		}
103		else
104		{
105	0	isSelected = selected;
106		}
107	0	displayLinks.add(new UrlLinkDisplay(key, entry.getValue(), isSelected,
108		isPrimary));
109		}
110	0	return displayLinks;
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	protected boolean isMiriamId(String id)...
114		{
115	0	return MIRIAM_PATTERN.matcher(id).matches();
116		}
117
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	@Override...
119		public boolean isUserEntry(String id)
120		{
121	0	return !isMiriamId(id);
122		}
123		}