Coverage Report
File Alignment.java
Coverage histogram
37% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| Alignment | 54 | 54 | 18 |
Contributing tests
This file is covered by 70 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.io.FileFormat; | |
| 25 | import jalview.io.FileFormatI; | |
| 26 | import jalview.io.FileFormats; | |
| 27 | import jalview.io.FormatAdapter; | |
| 28 | import jalview.ws.params.OptionI; | |
| 29 | import jalview.ws.params.simple.BooleanOption; | |
| 30 | import jalview.ws.params.simple.Option; | |
| 31 | import jalview.ws.rest.InputType; | |
| 32 | import jalview.ws.rest.NoValidInputDataException; | |
| 33 | import jalview.ws.rest.RestJob; | |
| 34 | ||
| 35 | import java.io.BufferedOutputStream; | |
| 36 | import java.io.File; | |
| 37 | import java.io.FileOutputStream; | |
| 38 | import java.io.OutputStreamWriter; | |
| 39 | import java.io.PrintWriter; | |
| 40 | import java.io.UnsupportedEncodingException; | |
| 41 | import java.util.ArrayList; | |
| 42 | import java.util.List; | |
| 43 | ||
| 44 | import org.apache.http.entity.mime.content.ContentBody; | |
| 45 | import org.apache.http.entity.mime.content.FileBody; | |
| 46 | import org.apache.http.entity.mime.content.StringBody; | |
| 47 | ||
| 48 | /** | |
| 49 | * format an alignment for input to rest service. | |
| 50 | * | |
| 51 | * @author JimP | |
| 52 | * | |
| 53 | */ | |
| 54 | public class Alignment extends InputType | |
| 55 | { | |
| 56 | 378 |  public Alignment() |
| 57 | { | |
| 58 | 378 | super(new Class[] { AlignmentI.class }); |
| 59 | } | |
| 60 | ||
| 61 | FileFormatI format = FileFormat.Fasta; | |
| 62 | ||
| 63 | molType type; | |
| 64 | ||
| 65 | boolean jvsuffix = false; | |
| 66 | ||
| 67 | /** | |
| 68 | * input data as a file upload rather than inline content | |
| 69 | */ | |
| 70 | public boolean writeAsFile = false; | |
| 71 | ||
| 72 | 2 | @Override |
| 73 | public ContentBody formatForInput(RestJob rj) | |
| 74 | throws UnsupportedEncodingException, NoValidInputDataException | |
| 75 | { | |
| 76 | 2 | AlignmentI alignment = rj.getAlignmentForInput(token, type); |
| 77 | 2 | if (writeAsFile) |
| 78 | { | |
| 79 | 2 | try |
| 80 | { | |
| 81 | 2 | File fa = File.createTempFile("jvmime", ".fa"); |
| 82 | 2 | PrintWriter pw = new PrintWriter(new OutputStreamWriter( |
| 83 | new BufferedOutputStream(new FileOutputStream(fa)), | |
| 84 | "UTF-8")); | |
| 85 | 2 | pw.append(new FormatAdapter().formatSequences(format, alignment, |
| 86 | jvsuffix)); | |
| 87 | 2 | pw.close(); |
| 88 | 2 | return new FileBody(fa, "text/plain"); |
| 89 | } catch (Exception ex) | |
| 90 | { | |
| 91 | 0 | throw new NoValidInputDataException( |
| 92 | "Couldn't write out alignment to file.", ex); | |
| 93 | } | |
| 94 | } | |
| 95 | else | |
| 96 | { | |
| 97 | 0 | FormatAdapter fa = new FormatAdapter(); |
| 98 | 0 | fa.setNewlineString("\r\n"); |
| 99 | 0 | return new StringBody( |
| 100 | (fa.formatSequences(format, alignment, jvsuffix))); | |
| 101 | // , | |
| 102 | // "text/plain",Charset.forName("UTF-8")); | |
| 103 | // , "text/plain", Charset.forName("UTF-8")); | |
| 104 | // sb.getContentTypeParameters().put("filename", "alignment.fa"); | |
| 105 | } | |
| 106 | } | |
| 107 | ||
| 108 | 26 | @Override |
| 109 | public List<String> getURLEncodedParameter() | |
| 110 | { | |
| 111 | 26 | List<String> prms = new ArrayList<String>(); |
| 112 | 26 | prms.add("format='" + format.getName() + "'"); |
| 113 | 26 | if (type != null) |
| 114 | { | |
| 115 | 0 | prms.add("type='" + type.toString() + "'"); |
| 116 | } | |
| 117 | 26 | if (jvsuffix) |
| 118 | { | |
| 119 | 0 | prms.add("jvsuffix"); |
| 120 | } | |
| 121 | 26 | if (writeAsFile) |
| 122 | { | |
| 123 | 26 | prms.add("writeasfile"); |
| 124 | } | |
| 125 | 26 | return prms; |
| 126 | } | |
| 127 | ||
| 128 | 383 | @Override |
| 129 | public String getURLtokenPrefix() | |
| 130 | { | |
| 131 | 383 | return "ALIGNMENT"; |
| 132 | } | |
| 133 | ||
| 134 | 370 | @Override |
| 135 | public boolean configureProperty(String tok, String val, | |
| 136 | StringBuffer warnings) | |
| 137 | { | |
| 138 | 370 | if (tok.startsWith("jvsuffix")) |
| 139 | { | |
| 140 | 0 | jvsuffix = true; |
| 141 | 0 | return true; |
| 142 | } | |
| 143 | 370 | if (tok.startsWith("writeasfile")) |
| 144 | { | |
| 145 | 185 | writeAsFile = true; |
| 146 | 185 | return true; |
| 147 | } | |
| 148 | ||
| 149 | 185 | if (tok.startsWith("format")) |
| 150 | { | |
| 151 | 185 | for (FileFormatI fmt : FileFormats.getInstance().getFormats()) |
| 152 | { | |
| 153 | 185 | if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName())) |
| 154 | { | |
| 155 | 185 | format = fmt; |
| 156 | 185 | return true; |
| 157 | } | |
| 158 | } | |
| 159 | 0 | warnings.append( |
| 160 | "Invalid alignment format '" + val + "'. Must be one of ("); | |
| 161 | 0 | for (String fmt : FileFormats.getInstance().getWritableFormats(true)) |
| 162 | { | |
| 163 | 0 | warnings.append(" ").append(fmt); |
| 164 | } | |
| 165 | 0 | warnings.append(")\n"); |
| 166 | } | |
| 167 | 0 | if (tok.startsWith("type")) |
| 168 | { | |
| 169 | 0 | try |
| 170 | { | |
| 171 | 0 | type = molType.valueOf(val); |
| 172 | 0 | return true; |
| 173 | } catch (Exception x) | |
| 174 | { | |
| 175 | 0 | warnings.append( |
| 176 | "Invalid molecule type '" + val + "'. Must be one of ("); | |
| 177 | 0 | for (molType v : molType.values()) |
| 178 | { | |
| 179 | 0 | warnings.append(" " + v); |
| 180 | } | |
| 181 | 0 | warnings.append(")\n"); |
| 182 | } | |
| 183 | } | |
| 184 | 0 | return false; |
| 185 | } | |
| 186 | ||
| 187 | 0 | @Override |
| 188 | public List<OptionI> getOptions() | |
| 189 | { | |
| 190 | 0 | List<OptionI> lst = getBaseOptions(); |
| 191 | 0 | lst.add(new BooleanOption("jvsuffix", |
| 192 | "Append jalview style /start-end suffix to ID", false, false, | |
| 193 | jvsuffix, null)); | |
| 194 | 0 | lst.add(new BooleanOption("writeasfile", |
| 195 | "Append jalview style /start-end suffix to ID", false, false, | |
| 196 | writeAsFile, null)); | |
| 197 | ||
| 198 | 0 | List<String> writable = FileFormats.getInstance() |
| 199 | .getWritableFormats(true); | |
| 200 | 0 | lst.add(new Option("format", "Alignment upload format", true, |
| 201 | FileFormat.Fasta.toString(), format.getName(), writable, null)); | |
| 202 | 0 | lst.add(createMolTypeOption("type", "Sequence type", false, type, |
| 203 | null)); | |
| 204 | ||
| 205 | 0 | return lst; |
| 206 | } | |
| 207 | ||
| 208 | } |