Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
BackupFilenameParts	25	48	24	0.621621662.2%	Show methods

Class BackupFilenameParts

Class BackupFilenameParts	Line # 25	Total Statements 48	Complexity 24	TOTAL Coverage 0.621621662.2%
BackupFilenameParts()   BackupFilenameParts()	3939	1.01	1.01	0.0 0.00%
BackupFilenameParts(File,String,String,int)   BackupFilenameParts(File,String,String,int)	4444	1.01	1.01	1.0 1.0100%
BackupFilenameParts(String,String,String,int)   BackupFilenameParts(String,String,String,int)	5050	1.01	1.01	1.0 1.0100%
BackupFilenameParts(String,String,String,int,boolean)   BackupFilenameParts(String,String,String,int,boolean)	5656	29.029	15.015	0.7111111 0.711111171.1%
currentBackupFilenameParts(String,String,boolean) : BackupFilenameParts   currentBackupFilenameParts(String,String,boolean) : BackupFilenameParts	131131	10.010	3.03	0.0 0.00%
isBackupFile() : boolean   isBackupFile() : boolean	154154	1.01	1.01	1.0 1.0100%
indexNum() : int   indexNum() : int	159159	1.01	1.01	1.0 1.0100%
getBackupFilename(int,String,String,int) : String   getBackupFilename(int,String,String,int) : String	164164	4.04	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.36486486	jalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignmentjalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignment	1PASS

 

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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.io;
22
23		import java.io.File;
24
		62.2% Uncovered Elements: 28 (74) Complexity: 24 Complexity Density: 0.5
25		public class BackupFilenameParts
26		{
27		private String base;
28
29		private String templateStart;
30
31		private int num;
32
33		private int digits;
34
35		private String templateEnd;
36
37		private boolean isBackupFile;
38
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
39	0	private BackupFilenameParts()...
40		{
41	0	this.isBackupFile = false;
42		}
43
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
44	1	public BackupFilenameParts(File file, String base, String template,...
45		int digits)
46		{
47	1	this(file.getName(), base, template, digits);
48		}
49
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
50	516	public BackupFilenameParts(String filename, String base, String template,...
51		int suggesteddigits)
52		{
53	516	this(filename, base, template, suggesteddigits, false);
54		}
55
		71.1% Uncovered Elements: 13 (45) Complexity: 15 Complexity Density: 0.52
56	516	public BackupFilenameParts(String filename, String base, String template,...
57		int suggesteddigits, boolean extensionMatch)
58		{
59	516	this.isBackupFile = false;
60
61	516	int numcharstart = template.indexOf(BackupFiles.NUM_PLACEHOLDER);
62	516	int digits = 0;
63	516	String templateStart = template;
64	516	String templateEnd = "";
65	516	if (numcharstart > -1)
66		{
67	516	templateStart = template.substring(0, numcharstart);
68	516	templateEnd = template.substring(
69		numcharstart + BackupFiles.NUM_PLACEHOLDER.length());
70	516	digits = suggesteddigits;
71		}
72
73	516	String savedFilename = "";
74		// if extensionOnly is set then reset the filename to the last occurrence of
75		// the extension+templateStart and try the match
76	516	if (extensionMatch)
77		{
78		// only trying to match from extension onwards
79
80	0	int extensioncharstart = filename
81		.lastIndexOf('.' + base + templateStart);
82	0	if (extensioncharstart == -1)
83		{
84	0	return;
85		}
86
87	0	savedFilename = filename.substring(0, extensioncharstart + 1); // include
88		// the "."
89	0	filename = filename.substring(extensioncharstart + 1);
90		}
91
92		// full filename match
93
94		// calculate minimum length of a backup filename
95	516	int minlength = base.length() + template.length()
96		- BackupFiles.NUM_PLACEHOLDER.length() + digits;
97
98	516	if (!(filename.startsWith(base + templateStart)
99		&& filename.endsWith(templateEnd)
100		&& filename.length() >= minlength))
101		{
102		// non-starter
103	514	return;
104		}
105
106	2	int startLength = base.length() + templateStart.length();
107	2	int endLength = templateEnd.length();
108	2	String numString = numcharstart > -1
109		? filename.substring(startLength, filename.length() - endLength)
110		: "";
111
112	2	if (filename.length() >= startLength + digits + endLength
113		&& filename.startsWith(base + templateStart)
114		&& filename.endsWith(templateEnd)
115		// match exactly digits number of number-characters (numString
116		// should be all digits and at least the right length), or more than
117		// digits long with proviso it's not zero-leading.
118		&& (numString.matches("[0-9]{" + digits + "}")
119		|| numString.matches("[1-9][0-9]{" + digits + ",}")))
120		{
121	2	this.base = extensionMatch ? savedFilename + base : base;
122	2	this.templateStart = templateStart;
123	2	this.num = numString.length() > 0 ? Integer.parseInt(numString) : 0;
124	2	this.digits = digits;
125	2	this.templateEnd = templateEnd;
126	2	this.isBackupFile = true;
127		}
128
129		}
130
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.3
131	0	public static BackupFilenameParts currentBackupFilenameParts(...
132		String filename, String base, boolean extensionMatch)
133		{
134	0	BackupFilenameParts bfp = new BackupFilenameParts();
135	0	BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
136		.getSavedBackupEntry();
137	0	String template = bfpe.suffix;
138	0	if (template == null)
139		{
140	0	return bfp;
141		}
142	0	int digits;
143	0	try
144		{
145	0	digits = bfpe.digits;
146		} catch (Exception e)
147		{
148	0	return bfp;
149		}
150	0	return new BackupFilenameParts(filename, base, template, digits,
151		extensionMatch);
152		}
153
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
154	515	public boolean isBackupFile()...
155		{
156	515	return this.isBackupFile;
157		}
158
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
159	1	public int indexNum()...
160		{
161	1	return this.num;
162		}
163
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
164	2	public static String getBackupFilename(int index, String base,...
165		String template, int digits)
166		{
167	2	String numString = String.format("%0" + digits + "d", index);
168	2	String backupSuffix = template.replaceFirst(BackupFiles.NUM_PLACEHOLDER,
169		numString);
170	2	String backupfilename = base + backupSuffix;
171	2	return backupfilename;
172		}
173		}