Coverage Report
File AnnotationFile.java
Coverage histogram
57% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AnnotationFile | 44 | 25 | 10 |
Contributing tests
This file is covered by 69 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 | 185 |  public AnnotationFile() |
| 47 | { | |
| 48 | 185 | 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 | @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 | @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 | 185 | @Override |
| 100 | public String getURLtokenPrefix() | |
| 101 | { | |
| 102 | 185 | return "ALANNOTATION"; |
| 103 | } | |
| 104 | ||
| 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 | ||
| 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 | } |