Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewLiteURLRetrieve	35	45	14	0.00%	Show methods

Class JalviewLiteURLRetrieve

Class JalviewLiteURLRetrieve	Line # 35	Total Statements 45	Complexity 14	TOTAL Coverage 0.00%
JalviewLiteURLRetrieve()   JalviewLiteURLRetrieve()	4343	1.01	1.01	0.0 0.00%
init() : void   init() : void	5353	44.044	13.013	0.0 0.00%

 

Contributing tests

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.bin;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.io.AppletFormatAdapter;
25		import jalview.io.DataSourceType;
26		import jalview.io.FileFormat;
27		import jalview.io.FileFormatI;
28		import jalview.io.FileFormats;
29		import jalview.io.FileParse;
30		import jalview.io.IdentifyFile;
31
32		import java.applet.Applet;
33		import java.io.InputStream;
34
		0% Uncovered Elements: 65 (65) Complexity: 14 Complexity Density: 0.31
35		public class JalviewLiteURLRetrieve extends Applet
36		{
37
38		private static final long serialVersionUID = 1L;
39
40		/**
41		* This is the default constructor
42		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
43	0	public JalviewLiteURLRetrieve()...
44		{
45	0	super();
46		}
47
48		/**
49		* This method initializes this
50		*
51		* @return void
52		*/
		0% Uncovered Elements: 62 (62) Complexity: 13 Complexity Density: 0.3
53	0	@Override...
54		public void init()
55		{
56	0	this.setSize(300, 200);
57	0	String file = getParameter("file");
58	0	if (file == null)
59		{
60	0	System.out
61		.println("Specify a resource to read on the file parameter");
62	0	return;
63		}
64	0	DataSourceType protocol = null;
65	0	try
66		{
67	0	jalview.bin.Console
68		.outPrintln("Loading thread started with:\n>>file\n" + file
69		+ ">>endfile");
70		// This might throw a security exception in certain browsers
71		// Netscape Communicator for instance.
72	0	try
73		{
74	0	boolean rtn = false;
75	0	InputStream is = getClass().getResourceAsStream("/" + file);
76	0	if (is != null)
77		{
78	0	rtn = true;
79	0	is.close();
80		}
81	0	jalview.bin.Console.errPrintln("Resource '" + file + "' was "
82	0	+ (rtn ? "" : "not") + " located by classloader.");
83	0	if (rtn)
84		{
85	0	protocol = DataSourceType.CLASSLOADER;
86		}
87
88		} catch (Exception ex)
89		{
90	0	jalview.bin.Console.outPrintln(
91		"Exception checking resources: " + file + " " + ex);
92		}
93	0	if (file.indexOf("://") > -1)
94		{
95	0	protocol = DataSourceType.URL;
96		}
97		else
98		{
99		// skipping codebase prepend check.
100	0	protocol = DataSourceType.FILE;
101		}
102
103	0	jalview.bin.Console.outPrintln("Trying to get contents of resource:");
104	0	FileParse fp = new FileParse(file, protocol);
105	0	if (fp.isValid())
106		{
107	0	String ln = null;
108	0	while ((ln = fp.nextLine()) != null)
109		{
110	0	System.out.print(ln);
111		}
112	0	fp.close();
113		}
114		else
115		{
116	0	jalview.bin.Console.outPrintln("Resource at " + file
117		+ " cannot be read with protocol==" + protocol);
118	0	return;
119		}
120	0	FileFormatI format = FileFormats.getInstance()
121		.forName(getParameter("format"));
122	0	if (format == null)
123		{
124	0	format = new IdentifyFile().identify(file, protocol);
125	0	jalview.bin.Console.outPrintln("Format is " + format);
126		}
127		else
128		{
129	0	jalview.bin.Console
130		.outPrintln("User specified Format is " + format);
131		}
132	0	AlignmentI al = null;
133	0	try
134		{
135	0	al = new AppletFormatAdapter().readFile(file, protocol, format);
136		} catch (java.io.IOException ex)
137		{
138	0	jalview.bin.Console.errPrintln("Failed to open the file.");
139	0	ex.printStackTrace();
140		}
141	0	if (al != null)
142		{
143	0	jalview.bin.Console.outPrintln(new AppletFormatAdapter()
144		.formatSequences(FileFormat.Fasta, al, false));
145		}
146		} catch (Exception e)
147		{
148	0	jalview.bin.Console.errPrintln("bailing out : Unexpected exception:");
149	0	e.printStackTrace();
150		}
151		}
152
153		}