2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.
23 import jalview.datamodel.DBRefEntry;
24 import jalview.datamodel.DBRefSource;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.gff.GffConstants;
28 import jalview.util.MessageManager;
29 import jalview.util.UrlLink;
31 import java.util.Arrays;
32 import java.util.Collection;
33 import java.util.Comparator;
34 import java.util.LinkedHashMap;
35 import java.util.List;
39 * generate HTML reports for a sequence
43 public class SequenceAnnotationReport
45 private static final String COMMA = ",";
47 private static final String ELLIPSIS = "...";
49 private static final int MAX_REFS_PER_SOURCE = 4;
51 private static final int MAX_SOURCES = 40;
53 private static final String[][] PRIMARY_SOURCES = new String[][] {
54 DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
55 DBRefSource.PROTEINDBS };
57 final String linkImageURL;
60 * Comparator to order DBRefEntry by Source + accession id (case-insensitive)
62 private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
66 public int compare(DBRefEntry ref1, DBRefEntry ref2)
68 String s1 = ref1.getSource();
69 String s2 = ref2.getSource();
70 boolean s1Primary = isPrimarySource(s1);
71 boolean s2Primary = isPrimarySource(s2);
72 if (s1Primary && !s2Primary)
76 if (!s1Primary && s2Primary)
80 int comp = s1 == null ? -1
81 : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
84 String a1 = ref1.getAccessionId();
85 String a2 = ref2.getAccessionId();
86 comp = a1 == null ? -1
87 : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
92 private boolean isPrimarySource(String source)
94 for (String[] primary : PRIMARY_SOURCES)
96 for (String s : primary)
108 public SequenceAnnotationReport(String linkImageURL)
110 this.linkImageURL = linkImageURL;
114 * Append text for the list of features to the tooltip
121 public void appendFeatures(final StringBuilder sb, int rpos,
122 List<SequenceFeature> features, Map<String, float[][]> minmax)
124 if (features != null)
126 for (SequenceFeature feature : features)
128 appendFeature(sb, rpos, minmax, feature);
134 * Appends the feature at rpos to the given buffer
141 void appendFeature(final StringBuilder sb, int rpos,
142 Map<String, float[][]> minmax, SequenceFeature feature)
144 if (feature.isContactFeature())
146 if (feature.getBegin() == rpos || feature.getEnd() == rpos)
152 sb.append(feature.getType()).append(" ").append(feature.getBegin())
153 .append(":").append(feature.getEnd());
162 // TODO: remove this hack to display link only features
163 boolean linkOnly = feature.getValue("linkonly") != null;
166 sb.append(feature.getType()).append(" ");
169 // we are marking a positional feature
170 sb.append(feature.begin);
172 if (feature.begin != feature.end)
174 sb.append(" ").append(feature.end);
177 if (feature.getDescription() != null
178 && !feature.description.equals(feature.getType()))
180 String tmpString = feature.getDescription();
181 String tmp2up = tmpString.toUpperCase();
182 int startTag = tmp2up.indexOf("<HTML>");
185 tmpString = tmpString.substring(startTag + 6);
186 tmp2up = tmp2up.substring(startTag + 6);
188 int endTag = tmp2up.indexOf("</BODY>");
191 tmpString = tmpString.substring(0, endTag);
192 tmp2up = tmp2up.substring(0, endTag);
194 endTag = tmp2up.indexOf("</HTML>");
197 tmpString = tmpString.substring(0, endTag);
202 sb.append("; ").append(tmpString);
206 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
208 // The description does not specify html is to
209 // be used, so we must remove < > symbols
210 tmpString = tmpString.replaceAll("<", "<");
211 tmpString = tmpString.replaceAll(">", ">");
214 sb.append(tmpString);
218 sb.append("; ").append(tmpString);
222 // check score should be shown
223 if (!Float.isNaN(feature.getScore()))
225 float[][] rng = (minmax == null) ? null
226 : minmax.get(feature.getType());
227 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
229 sb.append(" Score=").append(String.valueOf(feature.getScore()));
232 String status = (String) feature.getValue("status");
233 if (status != null && status.length() > 0)
235 sb.append("; (").append(status).append(")");
237 String clinSig = (String) feature
238 .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
241 sb.append("; ").append(clinSig);
248 * Format and appends any hyperlinks for the sequence feature to the string
254 void appendLinks(final StringBuffer sb, SequenceFeature feature)
256 if (feature.links != null)
258 if (linkImageURL != null)
260 sb.append(" <img src=\"" + linkImageURL + "\">");
264 for (String urlstring : feature.links)
268 for (List<String> urllink : createLinksFrom(null, urlstring))
270 sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
271 + urllink.get(0) + "\">"
272 + (urllink.get(0).toLowerCase()
273 .equals(urllink.get(1).toLowerCase())
275 : (urllink.get(0) + ":"
279 } catch (Exception x)
282 "problem when creating links from " + urlstring);
295 * @return Collection< List<String> > { List<String> { link target, link
296 * label, dynamic component inserted (if any), url }}
298 Collection<List<String>> createLinksFrom(SequenceI seq, String link)
300 Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
301 UrlLink urlLink = new UrlLink(link);
302 if (!urlLink.isValid())
304 System.err.println(urlLink.getInvalidMessage());
308 urlLink.createLinksFromSeq(seq, urlSets);
310 return urlSets.values();
313 public void createSequenceAnnotationReport(final StringBuilder tip,
314 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
315 Map<String, float[][]> minmax)
317 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
322 * Builds an html formatted report of sequence details and appends it to the
326 * buffer to append report to
328 * the sequence the report is for
330 * whether to include database references for the sequence
332 * whether to include non-positional sequence features
337 int createSequenceAnnotationReport(final StringBuilder sb,
338 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
339 Map<String, float[][]> minmax, boolean summary)
345 if (sequence.getDescription() != null)
347 tmp = sequence.getDescription();
348 sb.append("<br>").append(tmp);
349 maxWidth = Math.max(maxWidth, tmp.length());
351 SequenceI ds = sequence;
352 while (ds.getDatasetSequence() != null)
354 ds = ds.getDatasetSequence();
356 DBRefEntry[] dbrefs = ds.getDBRefs();
357 if (showDbRefs && dbrefs != null)
359 // note this sorts the refs held on the sequence!
360 Arrays.sort(dbrefs, comparator);
361 boolean ellipsis = false;
362 String source = null;
363 String lastSource = null;
364 int countForSource = 0;
366 boolean moreSources = false;
369 for (DBRefEntry ref : dbrefs)
371 source = ref.getSource();
377 boolean sourceChanged = !source.equals(lastSource);
384 if (sourceCount > MAX_SOURCES && summary)
392 if (countForSource == 1 || !summary)
396 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
398 String accessionId = ref.getAccessionId();
399 lineLength += accessionId.length() + 1;
400 if (countForSource > 1 && summary)
402 sb.append(", ").append(accessionId);
407 sb.append(source).append(" ").append(accessionId);
408 lineLength += source.length();
410 maxWidth = Math.max(maxWidth, lineLength);
412 if (countForSource == MAX_REFS_PER_SOURCE && summary)
414 sb.append(COMMA).append(ELLIPSIS);
420 sb.append("<br>").append(ELLIPSIS).append(COMMA).append(source)
421 .append(COMMA).append(ELLIPSIS);
426 sb.append(MessageManager.getString("label.output_seq_details"));
432 * add non-positional features if wanted
434 SequenceFeature[] features = sequence.getSequenceFeatures();
435 if (showNpFeats && features != null)
437 for (int i = 0; i < features.length; i++)
439 if (features[i].begin == 0 && features[i].end == 0)
441 int sz = -sb.length();
442 appendFeature(sb, 0, minmax, features[i]);
444 maxWidth = Math.max(maxWidth, sz);
452 public void createTooltipAnnotationReport(final StringBuilder tip,
453 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
454 Map<String, float[][]> minmax)
456 int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
457 showNpFeats, minmax, true);
461 // ? not sure this serves any useful purpose
462 // tip.insert(0, "<table width=350 border=0><tr><td>");
463 // tip.append("</td></tr></table>");