Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Alignment	54	54	18	0.00%	Show methods

Class Alignment

Class Alignment	Line # 54	Total Statements 54	Complexity 18	TOTAL Coverage 0.00%
Alignment()   Alignment()	5656	1.01	1.01	0.0 0.00%
formatForInput(RestJob) : ContentBody   formatForInput(RestJob) : ContentBody	7272	12.012	3.03	0.0 0.00%
getURLEncodedParameter() : List<String>   getURLEncodedParameter() : List<String>	108108	9.09	4.04	0.0 0.00%
getURLtokenPrefix() : String   getURLtokenPrefix() : String	128128	1.01	1.01	0.0 0.00%
configureProperty(String,String,StringBuffer) : boolean   configureProperty(String,String,StringBuffer) : boolean	134134	24.024	8.08	0.0 0.00%
getOptions() : List<OptionI>   getOptions() : List<OptionI>	187187	7.07	1.01	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.ws.rest.params;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.io.FileFormat;
25		import jalview.io.FileFormatI;
26		import jalview.io.FileFormats;
27		import jalview.io.FormatAdapter;
28		import jalview.ws.params.OptionI;
29		import jalview.ws.params.simple.BooleanOption;
30		import jalview.ws.params.simple.Option;
31		import jalview.ws.rest.InputType;
32		import jalview.ws.rest.NoValidInputDataException;
33		import jalview.ws.rest.RestJob;
34
35		import java.io.BufferedOutputStream;
36		import java.io.File;
37		import java.io.FileOutputStream;
38		import java.io.OutputStreamWriter;
39		import java.io.PrintWriter;
40		import java.io.UnsupportedEncodingException;
41		import java.util.ArrayList;
42		import java.util.List;
43
44		import org.apache.http.entity.mime.content.ContentBody;
45		import org.apache.http.entity.mime.content.FileBody;
46		import org.apache.http.entity.mime.content.StringBody;
47
48		/**
49		* format an alignment for input to rest service.
50		*
51		* @author JimP
52		*
53		*/
		0% Uncovered Elements: 78 (78) Complexity: 18 Complexity Density: 0.33
54		public class Alignment extends InputType
55		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	public Alignment()...
57		{
58	0	super(new Class[] { AlignmentI.class });
59		}
60
61		FileFormatI format = FileFormat.Fasta;
62
63		molType type;
64
65		boolean jvsuffix = false;
66
67		/**
68		* input data as a file upload rather than inline content
69		*/
70		public boolean writeAsFile = false;
71
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.25
72	0	@Override...
73		public ContentBody formatForInput(RestJob rj)
74		throws UnsupportedEncodingException, NoValidInputDataException
75		{
76	0	AlignmentI alignment = rj.getAlignmentForInput(token, type);
77	0	if (writeAsFile)
78		{
79	0	try
80		{
81	0	File fa = File.createTempFile("jvmime", ".fa");
82	0	PrintWriter pw = new PrintWriter(new OutputStreamWriter(
83		new BufferedOutputStream(new FileOutputStream(fa)),
84		"UTF-8"));
85	0	pw.append(new FormatAdapter().formatSequences(format, alignment,
86		jvsuffix));
87	0	pw.close();
88	0	return new FileBody(fa, "text/plain");
89		} catch (Exception ex)
90		{
91	0	throw new NoValidInputDataException(
92		"Couldn't write out alignment to file.", ex);
93		}
94		}
95		else
96		{
97	0	FormatAdapter fa = new FormatAdapter();
98	0	fa.setNewlineString("\r\n");
99	0	return new StringBody(
100		(fa.formatSequences(format, alignment, jvsuffix)));
101		// ,
102		// "text/plain",Charset.forName("UTF-8"));
103		// , "text/plain", Charset.forName("UTF-8"));
104		// sb.getContentTypeParameters().put("filename", "alignment.fa");
105		}
106		}
107
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.44
108	0	@Override...
109		public List<String> getURLEncodedParameter()
110		{
111	0	List<String> prms = new ArrayList<String>();
112	0	prms.add("format='" + format.getName() + "'");
113	0	if (type != null)
114		{
115	0	prms.add("type='" + type.toString() + "'");
116		}
117	0	if (jvsuffix)
118		{
119	0	prms.add("jvsuffix");
120		}
121	0	if (writeAsFile)
122		{
123	0	prms.add("writeasfile");
124		}
125	0	return prms;
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public String getURLtokenPrefix()
130		{
131	0	return "ALIGNMENT";
132		}
133
		0% Uncovered Elements: 34 (34) Complexity: 8 Complexity Density: 0.33
134	0	@Override...
135		public boolean configureProperty(String tok, String val,
136		StringBuffer warnings)
137		{
138	0	if (tok.startsWith("jvsuffix"))
139		{
140	0	jvsuffix = true;
141	0	return true;
142		}
143	0	if (tok.startsWith("writeasfile"))
144		{
145	0	writeAsFile = true;
146	0	return true;
147		}
148
149	0	if (tok.startsWith("format"))
150		{
151	0	for (FileFormatI fmt : FileFormats.getInstance().getFormats())
152		{
153	0	if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
154		{
155	0	format = fmt;
156	0	return true;
157		}
158		}
159	0	warnings.append(
160		"Invalid alignment format '" + val + "'. Must be one of (");
161	0	for (String fmt : FileFormats.getInstance().getWritableFormats(true))
162		{
163	0	warnings.append(" ").append(fmt);
164		}
165	0	warnings.append(")\n");
166		}
167	0	if (tok.startsWith("type"))
168		{
169	0	try
170		{
171	0	type = molType.valueOf(val);
172	0	return true;
173		} catch (Exception x)
174		{
175	0	warnings.append(
176		"Invalid molecule type '" + val + "'. Must be one of (");
177	0	for (molType v : molType.values())
178		{
179	0	warnings.append(" " + v);
180		}
181	0	warnings.append(")\n");
182		}
183		}
184	0	return false;
185		}
186
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
187	0	@Override...
188		public List<OptionI> getOptions()
189		{
190	0	List<OptionI> lst = getBaseOptions();
191	0	lst.add(new BooleanOption("jvsuffix",
192		"Append jalview style /start-end suffix to ID", false, false,
193		jvsuffix, null));
194	0	lst.add(new BooleanOption("writeasfile",
195		"Append jalview style /start-end suffix to ID", false, false,
196		writeAsFile, null));
197
198	0	List<String> writable = FileFormats.getInstance()
199		.getWritableFormats(true);
200	0	lst.add(new Option("format", "Alignment upload format", true,
201		FileFormat.Fasta.toString(), format.getName(), writable, null));
202	0	lst.add(createMolTypeOption("type", "Sequence type", false, type,
203		null));
204
205	0	return lst;
206		}
207
208		}