Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIRFile	30	69	24	0.675925967.6%	Show methods

Class PIRFile

Class PIRFile	Line # 30	Total Statements 69	Complexity 24	TOTAL Coverage 0.675925967.6%
PIRFile()   PIRFile()	3636	0.00	1.01	-1.0 -1.0 -
PIRFile(String,DataSourceType)   PIRFile(String,DataSourceType)	4040	1.01	1.01	0.0 0.00%
PIRFile(FileParse)   PIRFile(FileParse)	4646	1.01	1.01	1.0 1.0100%
parse() : void   parse() : void	5151	25.025	9.09	0.7692308 0.769230876.9%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	106106	42.042	12.012	0.61290324 0.6129032461.3%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.6759259	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		import jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceI;
25		import jalview.util.Comparison;
26
27		import java.io.IOException;
28		import java.util.Vector;
29
		67.6% Uncovered Elements: 35 (108) Complexity: 24 Complexity Density: 0.35
30		public class PIRFile extends AlignFile
31		{
32		public static boolean useModellerOutput = false;
33
34		Vector words = new Vector(); // Stores the words in a line after splitting
35
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
36	1	public PIRFile()...
37		{
38		}
39
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
40	0	public PIRFile(String inFile, DataSourceType sourceType)...
41		throws IOException
42		{
43	0	super(inFile, sourceType);
44		}
45
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
46	1	public PIRFile(FileParse source) throws IOException...
47		{
48	1	super(source);
49		}
50
		76.9% Uncovered Elements: 9 (39) Complexity: 9 Complexity Density: 0.36
51	1	@Override...
52		public void parse() throws IOException
53		{
54	1	StringBuffer sequence;
55	1	String line = null;
56	1	ModellerDescription md;
57
58	?	while ((line = nextLine()) != null)
59		{
60	15	if (line.length() == 0)
61		{
62		// jalview.bin.Console.outPrintln("blank line");
63	0	continue;
64		}
65	15	if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
66		{
67	0	continue;
68		}
69	15	Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
70
71	15	sequence = new StringBuffer();
72
73	15	newSeq.setDescription(nextLine()); // this is the title line
74
75	15	boolean starFound = false;
76
77	60	while (!starFound)
78		{
79	45	line = nextLine();
80	45	sequence.append(line);
81
82	45	if (line == null)
83		{
84	0	break;
85		}
86
87	45	if (line.indexOf("*") > -1)
88		{
89	15	starFound = true;
90		}
91		}
92
93	15	if (sequence.length() > 0)
94		{
95	15	sequence.setLength(sequence.length() - 1);
96	15	newSeq.setSequence(sequence.toString());
97
98	15	seqs.addElement(newSeq);
99
100	15	md = new ModellerDescription(newSeq.getDescription());
101	15	md.updateSequenceI(newSeq);
102		}
103		}
104		}
105
		61.3% Uncovered Elements: 24 (62) Complexity: 12 Complexity Density: 0.29
106	1	@Override...
107		public String print(SequenceI[] s, boolean jvsuffix)
108		{
109	1	boolean is_NA = Comparison.isNucleotide(s);
110	1	int len = 72;
111	1	StringBuffer out = new StringBuffer();
112	1	int i = 0;
113	1	ModellerDescription md;
114
115	16	while ((i < s.length) && (s[i] != null))
116		{
117	15	String seq = s[i].getSequenceAsString();
118	15	seq = seq + "*";
119
120	15	if (is_NA)
121		{
122		// modeller doesn't really do nucleotides, so we don't do anything fancy
123		// Official tags area as follows, for now we'll use P1 and DL
124		// Protein (complete) P1
125		// Protein (fragment) F1
126		// DNA (linear) Dl
127		// DNA (circular) DC
128		// RNA (linear) RL
129		// RNA (circular) RC
130		// tRNA N3
131		// other functional RNA N1
132
133	0	out.append(">N1;" + s[i].getName());
134	0	out.append(newline);
135	0	if (s[i].getDescription() == null)
136		{
137	0	out.append(s[i].getName() + " "
138		+ (s[i].getEnd() - s[i].getStart() + 1));
139	0	out.append(is_NA ? " bases" : " residues");
140	0	out.append(newline);
141		}
142		else
143		{
144	0	out.append(s[i].getDescription());
145	0	out.append(newline);
146		}
147		}
148		else
149		{
150
151	15	if (useModellerOutput)
152		{
153	0	out.append(">P1;" + s[i].getName());
154	0	out.append(newline);
155	0	md = new ModellerDescription(s[i]);
156	0	out.append(md.getDescriptionLine());
157	0	out.append(newline);
158		}
159		else
160		{
161	15	out.append(">P1;" + printId(s[i], jvsuffix));
162	15	out.append(newline);
163	15	if (s[i].getDescription() != null)
164		{
165	15	out.append(s[i].getDescription());
166	15	out.append(newline);
167		}
168		else
169		{
170	0	out.append(s[i].getName() + " "
171		+ (s[i].getEnd() - s[i].getStart() + 1) + " residues");
172	0	out.append(newline);
173		}
174		}
175		}
176	15	int nochunks = (seq.length() / len)
177	15	+ (seq.length() % len > 0 ? 1 : 0);
178
179	60	for (int j = 0; j < nochunks; j++)
180		{
181	45	int start = j * len;
182	45	int end = start + len;
183
184	45	if (end < seq.length())
185		{
186	30	out.append(seq.substring(start, end));
187	30	out.append(newline);
188		}
189	15	else if (start < seq.length())
190		{
191	15	out.append(seq.substring(start));
192	15	out.append(newline);
193		}
194		}
195
196	15	i++;
197		}
198
199	1	return out.toString();
200		}
201
202		}