2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 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 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.rest.params;
21 import jalview.datamodel.AlignmentI;
22 import jalview.datamodel.SequenceI;
23 import jalview.ws.params.OptionI;
24 import jalview.ws.params.simple.Option;
25 import jalview.ws.rest.InputType;
26 import jalview.ws.rest.NoValidInputDataException;
27 import jalview.ws.rest.RestJob;
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 * input a list of sequences separated by some separator
43 public class SeqVector extends InputType
52 { AlignmentI.class });
56 public ContentBody formatForInput(RestJob rj)
57 throws UnsupportedEncodingException, NoValidInputDataException
59 StringBuffer idvector = new StringBuffer();
61 for (SequenceI seq : rj.getSequencesForInput(token, type))
67 idvector.append(seq.getSequence());
69 return new StringBody(idvector.toString());
73 public List<String> getURLEncodedParameter()
75 ArrayList<String> prms = new ArrayList<String>();
76 super.addBaseParams(prms);
77 prms.add("sep='" + sep + "'");
80 prms.add("type='" + type + "'");
86 public String getURLtokenPrefix()
92 public boolean configureProperty(String tok, String val,
93 StringBuffer warnings)
96 if (tok.startsWith("sep"))
101 if (tok.startsWith("type"))
105 type = molType.valueOf(val);
107 } catch (Exception x)
109 warnings.append("Invalid molecule type '" + val
110 + "'. Must be one of (");
111 for (molType v : molType.values())
113 warnings.append(" " + v);
115 warnings.append(")\n");
122 public List<OptionI> getOptions()
124 List<OptionI> lst = getBaseOptions();
125 lst.add(new Option("sep",
126 "Separator character between elements of vector", true, ",",
127 sep, Arrays.asList(new String[]
128 { " ", ",", ";", "\t", "|" }), null));
129 lst.add(createMolTypeOption("type", "Sequence type", false, type,