Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PfamFile	32	61	25	0.00%	Show methods

Class PfamFile

Class PfamFile	Line # 32	Total Statements 61	Complexity 25	TOTAL Coverage 0.00%
PfamFile()   PfamFile()	3535	0.00	1.01	-1.0 -1.0 -
PfamFile(String,DataSourceType)   PfamFile(String,DataSourceType)	3939	1.01	1.01	0.0 0.00%
PfamFile(FileParse)   PfamFile(FileParse)	4545	1.01	1.01	0.0 0.00%
initData() : void   initData() : void	5050	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	5656	38.038	14.014	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	147147	20.020	7.07	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.io;
22
23		import jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceI;
25		import jalview.util.Format;
26		import jalview.util.MessageManager;
27
28		import java.io.IOException;
29		import java.util.ArrayList;
30		import java.util.HashMap;
31
		0% Uncovered Elements: 99 (99) Complexity: 25 Complexity Density: 0.41
32		public class PfamFile extends AlignFile
33		{
34
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
35	0	public PfamFile()...
36		{
37		}
38
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
39	0	public PfamFile(String inFile, DataSourceType sourceType)...
40		throws IOException
41		{
42	0	super(inFile, sourceType);
43		}
44
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
45	0	public PfamFile(FileParse source) throws IOException...
46		{
47	0	super(source);
48		}
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	@Override...
51		public void initData()
52		{
53	0	super.initData();
54		}
55
		0% Uncovered Elements: 62 (62) Complexity: 14 Complexity Density: 0.37
56	0	@Override...
57		public void parse() throws IOException
58		{
59	0	int i = 0;
60	0	String line;
61
62	0	HashMap<String, StringBuffer> seqhash = new HashMap<String, StringBuffer>();
63	0	ArrayList<String> headers = new ArrayList<String>();
64	0	boolean useTabs = false;
65	0	int spces;
66	0	while ((line = nextLine()) != null)
67		{
68	0	if (line.indexOf("#") == 0)
69		{
70		// skip comment lines
71	0	continue;
72		}
73		// locate first space or (if already checked), tab
74	0	if (useTabs)
75		{
76	0	spces = line.indexOf("\t");
77		}
78		else
79		{
80	0	spces = line.indexOf(" ");
81		// check to see if we ought to split on tabs instead.
82	0	if (!useTabs && spces == -1)
83		{
84	0	useTabs = true;
85	0	spces = line.indexOf("\t");
86		}
87		}
88	0	if (spces <= 0)
89		{
90		// no sequence data to split on
91	0	continue;
92		}
93	0	String id = line.substring(0, spces);
94	0	StringBuffer tempseq;
95
96	0	if (seqhash.containsKey(id))
97		{
98	0	tempseq = seqhash.get(id);
99		}
100		else
101		{
102	0	tempseq = new StringBuffer();
103	0	seqhash.put(id, tempseq);
104		}
105
106	0	if (!(headers.contains(id)))
107		{
108	0	headers.add(id);
109		}
110	0	if (spces + 1 < line.length())
111		{
112	0	tempseq.append(line.substring(spces + 1).trim());
113		}
114		}
115
116	0	this.noSeqs = headers.size();
117
118	0	if (noSeqs < 1)
119		{
120	0	throw new IOException(MessageManager
121		.getString("exception.pfam_no_sequences_found"));
122		}
123
124	0	for (i = 0; i < headers.size(); i++)
125		{
126	0	if (seqhash.get(headers.get(i)) != null)
127		{
128	0	if (maxLength < seqhash.get(headers.get(i)).toString().length())
129		{
130	0	maxLength = seqhash.get(headers.get(i)).toString().length();
131		}
132
133	0	Sequence newSeq = parseId(headers.get(i).toString());
134	0	newSeq.setSequence(
135		seqhash.get(headers.get(i).toString()).toString());
136	0	seqs.addElement(newSeq);
137		}
138		else
139		{
140	0	jalview.bin.Console
141		.errPrintln("PFAM File reader: Can't find sequence for "
142		+ headers.get(i));
143		}
144		}
145		}
146
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.35
147	0	@Override...
148		public String print(SequenceI[] s, boolean jvsuffix)
149		{
150	0	StringBuffer out = new StringBuffer("");
151
152	0	int max = 0;
153	0	int maxid = 0;
154
155	0	int i = 0;
156
157	0	while ((i < s.length) && (s[i] != null))
158		{
159	0	String tmp = printId(s[i], jvsuffix);
160
161	0	max = Math.max(max, s[i].getLength());
162
163	0	if (tmp.length() > maxid)
164		{
165	0	maxid = tmp.length();
166		}
167
168	0	i++;
169		}
170
171	0	if (maxid < 15)
172		{
173	0	maxid = 15;
174		}
175
176	0	int j = 0;
177
178	0	while ((j < s.length) && (s[j] != null))
179		{
180	0	out.append(new Format("%-" + maxid + "s")
181		.form(printId(s[j], jvsuffix) + " "));
182
183	0	out.append(s[j].getSequenceAsString());
184	0	out.append(newline);
185	0	j++;
186		}
187
188	0	out.append(newline);
189
190	0	return out.toString();
191		}
192		}