2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.rest.params;
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;
30 import java.io.UnsupportedEncodingException;
31 import java.util.ArrayList;
32 import java.util.Arrays;
33 import java.util.List;
35 import org.apache.http.entity.mime.content.ContentBody;
36 import org.apache.http.entity.mime.content.StringBody;
39 * format a jalview annotation file for input to a rest service.
44 public class AnnotationFile extends InputType
46 public AnnotationFile()
49 { AlignmentI.class });
53 * standard jalview annotation file
55 final String JVANNOT = "JalviewAnnotation";
58 * export annotation row as simple csv
60 final String CSVANNOT = "CsvAnnotationRow";
63 * format of annotation file
65 String format = JVANNOT;
67 // TODO verify annotation file format enumeration
69 public ContentBody formatForInput(RestJob rj)
70 throws UnsupportedEncodingException, NoValidInputDataException
72 AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
73 if (format.equals(JVANNOT))
75 return new StringBody(
76 new jalview.io.AnnotationFile().printAnnotations(
77 al.getAlignmentAnnotation(), al.getGroups(),
82 if (!format.equals(CSVANNOT))
84 throw new UnsupportedEncodingException(
85 "Unrecognised format for exporting Annotation (" + format
88 return new StringBody(
89 new jalview.io.AnnotationFile().printCSVAnnotations(al
90 .getAlignmentAnnotation()));
95 public List<String> getURLEncodedParameter()
97 ArrayList<String> prms = new ArrayList<String>();
98 super.addBaseParams(prms);
99 prms.add("format='" + format + "'");
104 public String getURLtokenPrefix()
106 return "ALANNOTATION";
110 public boolean configureProperty(String tok, String val,
111 StringBuffer warnings)
114 if (tok.startsWith("format"))
116 for (String fmt : new String[]
117 { CSVANNOT, JVANNOT })
119 if (val.equalsIgnoreCase(fmt))
125 warnings.append("Invalid annotation file format '" + val
126 + "'. Must be one of (");
127 for (String fmt : new String[]
128 { CSVANNOT, JVANNOT })
130 warnings.append(" " + fmt);
132 warnings.append(")\n");
138 public List<OptionI> getOptions()
140 // TODO - consider disregarding base options here.
141 List<OptionI> lst = getBaseOptions();
142 lst.add(new Option("format", "Alignment annotation upload format",
143 true, JVANNOT, format, Arrays.asList(new String[]
144 { JVANNOT, CSVANNOT }), null));