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Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.ws.rest.params

File AnnotationFile.java

 

Coverage histogram

../../../../img/srcFileCovDistChart1.png
57% of files have more coverage

Code metrics

8
25
6
1
141
91
10
0.4
4.17
6
1.67

Classes

Class Line # Actions
AnnotationFile 44 25 10
0.10256410410.3%
 

Contributing tests

This file is covered by 300 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.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    */
 
44    public class AnnotationFile extends InputType
45    {
 
46  8254 toggle public AnnotationFile()
47    {
48  8254 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
 
67  0 toggle @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   
 
90  0 toggle @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   
 
99  8254 toggle @Override
100    public String getURLtokenPrefix()
101    {
102  8254 return "ALANNOTATION";
103    }
104   
 
105  0 toggle @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   
 
131  0 toggle @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    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.