Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewFileFilter	32	54	34	0.588235358.8%	Show methods

Class JalviewFileFilter

Class JalviewFileFilter	Line # 32	Total Statements 54	Complexity 34	TOTAL Coverage 0.588235358.8%
JalviewFileFilter(String,String)   JalviewFileFilter(String,String)	4646	4.04	2.02	1.0 1.0100%
JalviewFileFilter(String[])   JalviewFileFilter(String[])	5858	1.01	1.01	0.0 0.00%
JalviewFileFilter(String[],String)   JalviewFileFilter(String[],String)	6363	4.04	3.03	0.0 0.00%
getAcceptableExtension() : String   getAcceptableExtension() : String	7777	1.01	1.01	0.0 0.00%
accept(File) : boolean   accept(File) : boolean	8383	16.016	10.010	0.4 0.440%
getExtension(File) : String   getExtension(File) : String	128128	7.07	4.04	0.90909094 0.9090909490.9%
addExtension(String) : void   addExtension(String) : void	146146	4.04	2.02	1.0 1.0100%
getDescription() : String   getDescription() : String	157157	11.011	7.07	0.7619048 0.761904876.2%
setDescription(String) : void   setDescription(String) : void	191191	2.02	1.01	1.0 1.0100%
setExtensionListInDescription(boolean) : void   setExtensionListInDescription(boolean) : void	197197	2.02	1.01	0.0 0.00%
isExtensionListInDescription() : boolean   isExtensionListInDescription() : boolean	203203	1.01	1.01	1.0 1.0100%
setParentJFC(JalviewFileChooser) : void   setParentJFC(JalviewFileChooser) : void	208208	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5882353	jalview.schemes.ColourSchemesTest.testGetColourSchemejalview.schemes.ColourSchemesTest.testGetColourScheme	1PASS
	0.5882353	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	1PASS
	0.5882353	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.5882353	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.5882353	jalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessagejalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessage	1PASS
	0.5882353	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.5882353	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	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.io;
22
23		import java.io.File;
24		import java.util.Hashtable;
25		import java.util.Iterator;
26		import java.util.LinkedHashMap;
27		import java.util.Map;
28		import java.util.StringTokenizer;
29
30		import javax.swing.filechooser.FileFilter;
31
		58.8% Uncovered Elements: 42 (102) Complexity: 34 Complexity Density: 0.63
32		public class JalviewFileFilter extends FileFilter
33		{
34		public static Hashtable suffixHash = new Hashtable();
35
36		private Map<String, JalviewFileFilter> filters = null;
37
38		private String description = "no description";
39
40		private String fullDescription = "full description";
41
42		private boolean useExtensionsInDescription = true;
43
44		private JalviewFileChooser parentJFC = null;
45
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
46	306	public JalviewFileFilter(String extension, String description)...
47		{
48	306	StringTokenizer st = new StringTokenizer(extension, ",");
49
50	756	while (st.hasMoreElements())
51		{
52	450	addExtension(st.nextToken().trim());
53		}
54
55	306	setDescription(description);
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	public JalviewFileFilter(String[] filts)...
59		{
60	0	this(filts, null);
61		}
62
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
63	0	public JalviewFileFilter(String[] filts, String description)...
64		{
65	0	for (int i = 0; i < filts.length; i++)
66		{
67		// add filters one by one
68	0	addExtension(filts[i]);
69		}
70
71	0	if (description != null)
72		{
73	0	setDescription(description);
74		}
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	public String getAcceptableExtension()...
78		{
79	0	return filters.keySet().iterator().next().toString();
80		}
81
82		// takes account of the fact that database is a directory
		40% Uncovered Elements: 18 (30) Complexity: 10 Complexity Density: 0.62
83	233	@Override...
84		public boolean accept(File f)
85		{
86
87	233	if (f != null)
88		{
89	233	String extension = getExtension(f);
90
91	233	if (f.isDirectory())
92		{
93	191	return true;
94		}
95
96	42	if ((extension != null) && (filters.get(extension) != null))
97		{
98	0	return true;
99		}
100
101		}
102
103	42	if (parentJFC != null && parentJFC.includeBackupFiles)
104		{
105	0	Iterator<String> it = filters.keySet().iterator();
106	0	EXTENSION: while (it.hasNext())
107		{
108	0	String ext = it.next();
109
110		// quick negative test
111	0	if (!f.getName().contains(ext))
112		{
113	0	continue EXTENSION;
114		}
115
116	0	BackupFilenameParts bfp = BackupFilenameParts
117		.currentBackupFilenameParts(f.getName(), ext, true);
118	0	if (bfp.isBackupFile())
119		{
120	0	return true;
121		}
122		}
123		}
124
125	42	return false;
126		}
127
		90.9% Uncovered Elements: 1 (11) Complexity: 4 Complexity Density: 0.57
128	233	public String getExtension(File f)...
129		{
130	233	if (f != null)
131		{
132	233	String filename = f.getName();
133	233	int i = filename.lastIndexOf('.');
134
135	233	if ((i > 0) && (i < (filename.length() - 1)))
136		{
137	64	return filename.substring(i + 1).toLowerCase();
138		}
139
140	169	;
141		}
142
143	169	return "";
144		}
145
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
146	450	public void addExtension(String extension)...
147		{
148	450	if (filters == null)
149		{
150	306	filters = new LinkedHashMap<>(5);
151		}
152
153	450	filters.put(extension.toLowerCase(), this);
154	450	fullDescription = null;
155		}
156
		76.2% Uncovered Elements: 5 (21) Complexity: 7 Complexity Density: 0.64
157	306	@Override...
158		public String getDescription()
159		{
160	306	if (fullDescription == null)
161		{
162	306	if ((description == null) || isExtensionListInDescription())
163		{
164	306	fullDescription = (description == null) ? "("
165		: (description + " (");
166
167		// build the description from the extension list
168	306	Iterator<String> extensions = filters.keySet().iterator();
169
170	306	if (extensions != null)
171		{
172	306	fullDescription += ("." + extensions.next());
173
174	450	while (extensions.hasNext())
175		{
176	144	fullDescription += (", " + extensions.next());
177		}
178		}
179
180	306	fullDescription += ")";
181		}
182		else
183		{
184	0	fullDescription = description;
185		}
186		}
187
188	306	return fullDescription;
189		}
190
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
191	306	public void setDescription(String description)...
192		{
193	306	this.description = description;
194	306	fullDescription = null;
195		}
196
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
197	0	public void setExtensionListInDescription(boolean b)...
198		{
199	0	useExtensionsInDescription = b;
200	0	fullDescription = null;
201		}
202
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
203	306	public boolean isExtensionListInDescription()...
204		{
205	306	return useExtensionsInDescription;
206		}
207
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
208	0	protected void setParentJFC(JalviewFileChooser p)...
209		{
210	0	this.parentJFC = p;
211		}
212
213		}