Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationFile	44	25	10	0.00%	Show methods

Class AnnotationFile

Class AnnotationFile	Line # 44	Total Statements 25	Complexity 10	TOTAL Coverage 0.00%
AnnotationFile()   AnnotationFile()	4646	1.01	1.01	0.0 0.00%
formatForInput(RestJob) : ContentBody   formatForInput(RestJob) : ContentBody	6767	6.06	3.03	0.0 0.00%
getURLEncodedParameter() : List<String>   getURLEncodedParameter() : List<String>	9090	4.04	1.01	0.0 0.00%
getURLtokenPrefix() : String   getURLtokenPrefix() : String	9999	1.01	1.01	0.0 0.00%
configureProperty(String,String,StringBuffer) : boolean   configureProperty(String,String,StringBuffer) : boolean	105105	10.010	3.03	0.0 0.00%
getOptions() : List<OptionI>   getOptions() : List<OptionI>	131131	3.03	1.01	0.0 0.00%

 

Contributing tests

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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.ws.params.OptionI;
25		import jalview.ws.params.simple.Option;
26		import jalview.ws.rest.InputType;
27		import jalview.ws.rest.NoValidInputDataException;
28		import jalview.ws.rest.RestJob;
29
30		import java.io.UnsupportedEncodingException;
31		import java.util.ArrayList;
32		import java.util.Arrays;
33		import java.util.List;
34
35		import org.apache.http.entity.mime.content.ContentBody;
36		import org.apache.http.entity.mime.content.StringBody;
37
38		/**
39		* format a jalview annotation file for input to a rest service.
40		*
41		* @author JimP
42		*
43		*/
		0% Uncovered Elements: 39 (39) Complexity: 10 Complexity Density: 0.4
44		public class AnnotationFile extends InputType
45		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public AnnotationFile()...
47		{
48	0	super(new Class[] { AlignmentI.class });
49		}
50
51		/**
52		* standard jalview annotation file
53		*/
54		final String JVANNOT = "JalviewAnnotation";
55
56		/**
57		* export annotation row as simple csv
58		*/
59		final String CSVANNOT = "CsvAnnotationRow";
60
61		/**
62		* format of annotation file
63		*/
64		String format = JVANNOT;
65
66		// TODO verify annotation file format enumeration
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
67	0	@Override...
68		public ContentBody formatForInput(RestJob rj)
69		throws UnsupportedEncodingException, NoValidInputDataException
70		{
71	0	AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
72	0	if (format.equals(JVANNOT))
73		{
74	0	return new StringBody(new jalview.io.AnnotationFile()
75		.printAnnotationsForAlignment(al));
76		}
77		else
78		{
79	0	if (!format.equals(CSVANNOT))
80		{
81	0	throw new UnsupportedEncodingException(
82		"Unrecognised format for exporting Annotation (" + format
83		+ ")");
84		}
85	0	return new StringBody(new jalview.io.AnnotationFile()
86		.printCSVAnnotations(al.getAlignmentAnnotation()));
87		}
88		}
89
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
90	0	@Override...
91		public List<String> getURLEncodedParameter()
92		{
93	0	ArrayList<String> prms = new ArrayList<String>();
94	0	super.addBaseParams(prms);
95	0	prms.add("format='" + format + "'");
96	0	return prms;
97		}
98
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		public String getURLtokenPrefix()
101		{
102	0	return "ALANNOTATION";
103		}
104
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
105	0	@Override...
106		public boolean configureProperty(String tok, String val,
107		StringBuffer warnings)
108		{
109
110	0	if (tok.startsWith("format"))
111		{
112	0	for (String fmt : new String[] { CSVANNOT, JVANNOT })
113		{
114	0	if (val.equalsIgnoreCase(fmt))
115		{
116	0	format = fmt;
117	0	return true;
118		}
119		}
120	0	warnings.append("Invalid annotation file format '" + val
121		+ "'. Must be one of (");
122	0	for (String fmt : new String[] { CSVANNOT, JVANNOT })
123		{
124	0	warnings.append(" " + fmt);
125		}
126	0	warnings.append(")\n");
127		}
128	0	return false;
129		}
130
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
131	0	@Override...
132		public List<OptionI> getOptions()
133		{
134		// TODO - consider disregarding base options here.
135	0	List<OptionI> lst = getBaseOptions();
136	0	lst.add(new Option("format", "Alignment annotation upload format", true,
137		JVANNOT, format, Arrays.asList(new String[]
138		{ JVANNOT, CSVANNOT }), null));
139	0	return lst;
140		}
141		}