1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 *******************************************************************************/
18 package jalview.ws.rest.params;
20 import jalview.datamodel.AlignmentI;
21 import jalview.ws.params.OptionI;
22 import jalview.ws.params.simple.Option;
23 import jalview.ws.rest.InputType;
24 import jalview.ws.rest.NoValidInputDataException;
25 import jalview.ws.rest.RestJob;
26 import jalview.ws.rest.RestServiceDescription;
27 import jalview.ws.rest.InputType.molType;
29 import java.io.UnsupportedEncodingException;
30 import java.util.ArrayList;
31 import java.util.Arrays;
32 import java.util.List;
34 import org.apache.http.entity.mime.content.ContentBody;
35 import org.apache.http.entity.mime.content.StringBody;
38 * format a jalview annotation file for input to a rest service.
42 public class AnnotationFile extends InputType {
43 public AnnotationFile()
45 super(new Class[] { AlignmentI.class} );
48 * standard jalview annotation file
50 final String JVANNOT="JalviewAnnotation";
52 * export annotation row as simple csv
54 final String CSVANNOT="CsvAnnotationRow";
56 * format of annotation file
58 String format=JVANNOT;
59 // TODO verify annotation file format enumeration
61 public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
63 AlignmentI al = rj.getAlignmentForInput(token,molType.MIX);
64 if (format.equals(JVANNOT))
65 {return new StringBody(new jalview.io.AnnotationFile().printAnnotations(al.getAlignmentAnnotation(),
66 al.getGroups(),al.getProperties()));
68 if (!format.equals(CSVANNOT))
70 throw new UnsupportedEncodingException("Unrecognised format for exporting Annotation ("+format+")");
72 return new StringBody(new jalview.io.AnnotationFile().printCSVAnnotations(al.getAlignmentAnnotation()));
76 public List<String> getURLEncodedParameter()
78 ArrayList<String> prms = new ArrayList<String>();
79 super.addBaseParams(prms);
80 prms.add("format='"+format+"'");
84 public String getURLtokenPrefix()
86 return "ALANNOTATION";
89 public boolean configureProperty(String tok, String val,
90 StringBuffer warnings)
93 if (tok.startsWith("format"))
95 for (String fmt : new String[] { CSVANNOT, JVANNOT})
97 if (val.equalsIgnoreCase(fmt))
103 warnings.append("Invalid annotation file format '" + val
104 + "'. Must be one of (");
105 for (String fmt : new String[] { CSVANNOT, JVANNOT})
107 warnings.append(" " + fmt);
109 warnings.append(")\n");
114 public List<OptionI> getOptions()
116 // TODO - consider disregarding base options here.
117 List<OptionI> lst = getBaseOptions();
118 lst.add(new Option("format",
119 "Alignment annotation upload format", true, JVANNOT,
120 format, Arrays.asList(new String[]
121 { JVANNOT, CSVANNOT}), null));