Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PileUpfile	43	60	20	0.922222292.2%	Show methods

Class PileUpfile

Class PileUpfile	Line # 43	Total Statements 60	Complexity 20	TOTAL Coverage 0.922222292.2%
PileUpfile()   PileUpfile()	4949	0.00	1.01	-1.0 -1.0 -
PileUpfile(String,DataSourceType)   PileUpfile(String,DataSourceType)	6464	1.01	1.01	0.0 0.00%
PileUpfile(FileParse)   PileUpfile(FileParse)	7070	1.01	1.01	1.0 1.0100%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	7575	58.058	17.017	0.9404762 0.940476294%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.9222222	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	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		/**
24		* <p>
25		* Title:
26		* </p>
27		* PileUpfile
28		* <p>
29		* Description:
30		* </p>
31		*
32		* Read and write PileUp style MSF Files. This used to be the MSFFile class, and
33		* was written according to the EBI's idea of a subset of the MSF alignment
34		* format. But, that was updated to reflect current GCG style IO fashion, as
35		* found in Emboss (thanks David Martin!)
36		*
37		*/
38		import jalview.datamodel.SequenceI;
39		import jalview.util.Format;
40
41		import java.io.IOException;
42
		92.2% Uncovered Elements: 7 (90) Complexity: 20 Complexity Density: 0.33
43		public class PileUpfile extends MSFfile
44		{
45
46		/**
47		* Creates a new MSFfile object.
48		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
49	2	public PileUpfile()...
50		{
51		}
52
53		/**
54		* Creates a new MSFfile object.
55		*
56		* @param inFile
57		* DOCUMENT ME!
58		* @param sourceType
59		* DOCUMENT ME!
60		*
61		* @throws IOException
62		* DOCUMENT ME!
63		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	public PileUpfile(String inFile, DataSourceType sourceType)...
65		throws IOException
66		{
67	0	super(inFile, sourceType);
68		}
69
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
70	1	public PileUpfile(FileParse source) throws IOException...
71		{
72	1	super(source);
73		}
74
		94% Uncovered Elements: 5 (84) Complexity: 17 Complexity Density: 0.29
75	2	@Override...
76		public String print(SequenceI[] s, boolean jvsuffix)
77		{
78	2	StringBuffer out = new StringBuffer("PileUp");
79	2	out.append(newline);
80	2	out.append(newline);
81
82	2	int max = 0;
83	2	int maxid = 0;
84
85	2	int i = 0;
86	2	int bigChecksum = 0;
87	2	int[] checksums = new int[s.length];
88	32	while (i < s.length)
89		{
90	30	checksums[i] = checkSum(s[i].getSequenceAsString());
91	30	bigChecksum += checksums[i];
92	30	i++;
93		}
94
95	2	out.append(" MSF: " + s[0].getLength() + " Type: P Check: "
96		+ bigChecksum % 10000 + " ..");
97	2	out.append(newline);
98	2	out.append(newline);
99	2	out.append(newline);
100
101	2	i = 0;
102	32	while ((i < s.length) && (s[i] != null))
103		{
104	30	String seq = s[i].getSequenceAsString();
105	30	out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
106		+ seq.length() + " Check: " + checksums[i]
107		+ " Weight: 1.00");
108	30	out.append(newline);
109
110	30	if (seq.length() > max)
111		{
112	2	max = seq.length();
113		}
114
115	30	if (s[i].getName().length() > maxid)
116		{
117	6	maxid = s[i].getName().length();
118		}
119
120	30	i++;
121		}
122
123	2	if (maxid < 10)
124		{
125	0	maxid = 10;
126		}
127
128	2	maxid++;
129	2	out.append(newline);
130	2	out.append(newline);
131	2	out.append("//");
132	2	out.append(newline);
133	2	out.append(newline);
134
135	2	int len = 50;
136
137	2	int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
138
139	10	for (i = 0; i < nochunks; i++)
140		{
141	8	int j = 0;
142
143	128	while ((j < s.length) && (s[j] != null))
144		{
145	120	String name = printId(s[j], jvsuffix);
146
147	120	out.append(new Format("%-" + maxid + "s").form(name + " "));
148
149	720	for (int k = 0; k < 5; k++)
150		{
151	600	int start = (i * 50) + (k * 10);
152	600	int end = start + 10;
153
154	600	int length = s[j].getLength();
155	600	if ((end < length) && (start < length))
156		{
157	450	out.append(s[j].getSequence(start, end));
158
159	450	if (k < 4)
160		{
161	360	out.append(" ");
162		}
163		else
164		{
165	90	out.append(newline);
166		}
167		}
168		else
169		{
170	150	if (start < length)
171		{
172	30	out.append(s[j].getSequenceAsString().substring(start));
173	30	out.append(newline);
174		}
175		else
176		{
177	120	if (k == 0)
178		{
179	0	out.append(newline);
180		}
181		}
182		}
183		}
184
185	120	j++;
186		}
187
188	8	out.append(newline);
189		}
190
191	2	return out.toString();
192		}
193		}