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.api.FeatureColourI;
24 import jalview.datamodel.DBRefEntry;
25 import jalview.datamodel.DBRefSource;
26 import jalview.datamodel.GeneLociI;
27 import jalview.datamodel.MappedFeatures;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.util.MessageManager;
31 import jalview.util.StringUtils;
32 import jalview.util.UrlLink;
33 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
35 import java.util.Arrays;
36 import java.util.Collection;
37 import java.util.Comparator;
38 import java.util.LinkedHashMap;
39 import java.util.List;
43 * generate HTML reports for a sequence
47 public class SequenceAnnotationReport
49 private static final String COMMA = ",";
51 private static final String ELLIPSIS = "...";
53 private static final int MAX_REFS_PER_SOURCE = 4;
55 private static final int MAX_SOURCES = 40;
57 // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
59 final String linkImageURL;
62 * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
63 * with 'Primary' sources placed before others, and 'chromosome' first of all
65 private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
69 public int compare(DBRefEntry ref1, DBRefEntry ref2)
71 if (ref1 instanceof GeneLociI)
75 if (ref2 instanceof GeneLociI)
79 String s1 = ref1.getSource();
80 String s2 = ref2.getSource();
81 boolean s1Primary = DBRefSource.isPrimarySource(s1);
82 boolean s2Primary = DBRefSource.isPrimarySource(s2);
83 if (s1Primary && !s2Primary)
87 if (!s1Primary && s2Primary)
91 int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
92 .compareToIgnoreCase(s2));
95 String a1 = ref1.getAccessionId();
96 String a2 = ref2.getAccessionId();
97 comp = a1 == null ? -1 : (a2 == null ? 1 : a1
98 .compareToIgnoreCase(a2));
103 // private boolean isPrimarySource(String source)
105 // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
107 // for (String s : primary)
109 // if (source.equals(s))
119 public SequenceAnnotationReport(String linkURL)
121 this.linkImageURL = linkURL;
125 * Append text for the list of features to the tooltip
132 public void appendFeatures(final StringBuilder sb, int residuePos,
133 List<SequenceFeature> features, FeatureRendererModel fr)
135 for (SequenceFeature feature : features)
137 appendFeature(sb, residuePos, fr, feature, null);
142 * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
149 public void appendFeatures(StringBuilder sb, int residuePos,
150 MappedFeatures mf, FeatureRendererModel fr)
152 for (SequenceFeature feature : mf.features)
154 appendFeature(sb, residuePos, fr, feature, mf);
159 * Appends the feature at rpos to the given buffer
166 void appendFeature(final StringBuilder sb, int rpos,
167 FeatureRendererModel fr, SequenceFeature feature,
170 if (feature.isContactFeature())
172 if (feature.getBegin() == rpos || feature.getEnd() == rpos)
178 sb.append(feature.getType()).append(" ").append(feature.getBegin())
179 .append(":").append(feature.getEnd());
188 // TODO: remove this hack to display link only features
189 boolean linkOnly = feature.getValue("linkonly") != null;
192 sb.append(feature.getType()).append(" ");
195 // we are marking a positional feature
196 sb.append(feature.begin);
198 if (feature.begin != feature.end)
200 sb.append(" ").append(feature.end);
203 String description = feature.getDescription();
204 if (description != null && !description.equals(feature.getType()))
206 description = StringUtils.stripHtmlTags(description);
207 sb.append("; ").append(description);
210 if (showScore(feature, fr))
212 sb.append(" Score=").append(String.valueOf(feature.getScore()));
214 String status = (String) feature.getValue("status");
215 if (status != null && status.length() > 0)
217 sb.append("; (").append(status).append(")");
221 * add attribute value if coloured by attribute
225 FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
226 if (fc != null && fc.isColourByAttribute())
228 String[] attName = fc.getAttributeName();
229 String attVal = feature.getValueAsString(attName);
232 sb.append("; ").append(String.join(":", attName)).append("=")
240 String variants = mf.findProteinVariants(feature);
241 if (!variants.isEmpty())
243 sb.append(" ").append(variants);
250 * Answers true if score should be shown, else false. Score is shown if it is
251 * not NaN, and the feature type has a non-trivial min-max score range
253 boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
255 if (Float.isNaN(feature.getScore()))
263 float[][] minMax = fr.getMinMax().get(feature.getType());
266 * minMax[0] is the [min, max] score range for positional features
268 if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
276 * Format and appends any hyperlinks for the sequence feature to the string
282 void appendLinks(final StringBuffer sb, SequenceFeature feature)
284 if (feature.links != null)
286 if (linkImageURL != null)
288 sb.append(" <img src=\"" + linkImageURL + "\">");
292 for (String urlstring : feature.links)
296 for (List<String> urllink : createLinksFrom(null, urlstring))
298 sb.append("<br/> <a href=\""
303 + (urllink.get(0).toLowerCase()
304 .equals(urllink.get(1).toLowerCase()) ? urllink
305 .get(0) : (urllink.get(0) + ":" + urllink
306 .get(1))) + "</a></br>");
308 } catch (Exception x)
310 System.err.println("problem when creating links from "
324 * @return Collection< List<String> > { List<String> { link target, link
325 * label, dynamic component inserted (if any), url }}
327 Collection<List<String>> createLinksFrom(SequenceI seq, String link)
329 Map<String, List<String>> urlSets = new LinkedHashMap<>();
330 UrlLink urlLink = new UrlLink(link);
331 if (!urlLink.isValid())
333 System.err.println(urlLink.getInvalidMessage());
337 urlLink.createLinksFromSeq(seq, urlSets);
339 return urlSets.values();
342 public void createSequenceAnnotationReport(final StringBuilder tip,
343 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
344 FeatureRendererModel fr)
346 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
351 * Builds an html formatted report of sequence details and appends it to the
355 * buffer to append report to
357 * the sequence the report is for
359 * whether to include database references for the sequence
361 * whether to include non-positional sequence features
366 int createSequenceAnnotationReport(final StringBuilder sb,
367 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
368 FeatureRendererModel fr, boolean summary)
374 if (sequence.getDescription() != null)
376 tmp = sequence.getDescription();
377 sb.append("<br>").append(tmp);
378 maxWidth = Math.max(maxWidth, tmp.length());
380 SequenceI ds = sequence;
381 while (ds.getDatasetSequence() != null)
383 ds = ds.getDatasetSequence();
388 maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
392 * add non-positional features if wanted
396 for (SequenceFeature sf : sequence.getFeatures()
397 .getNonPositionalFeatures())
399 int sz = -sb.length();
400 appendFeature(sb, 0, fr, sf, null);
402 maxWidth = Math.max(maxWidth, sz);
410 * A helper method that appends any DBRefs, returning the maximum line length
418 protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
421 List<DBRefEntry> dbrefs = ds.getDBRefs();
427 // note this sorts the refs held on the sequence!
428 dbrefs.sort(comparator);
429 boolean ellipsis = false;
430 String source = null;
431 String lastSource = null;
432 int countForSource = 0;
434 boolean moreSources = false;
435 int maxLineLength = 0;
438 for (DBRefEntry ref : dbrefs)
440 source = ref.getSource();
446 boolean sourceChanged = !source.equals(lastSource);
453 if (sourceCount > MAX_SOURCES && summary)
461 if (countForSource == 1 || !summary)
465 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
467 String accessionId = ref.getAccessionId();
468 lineLength += accessionId.length() + 1;
469 if (countForSource > 1 && summary)
471 sb.append(", ").append(accessionId);
476 sb.append(source).append(" ").append(accessionId);
477 lineLength += source.length();
479 maxLineLength = Math.max(maxLineLength, lineLength);
481 if (countForSource == MAX_REFS_PER_SOURCE && summary)
483 sb.append(COMMA).append(ELLIPSIS);
489 sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
494 sb.append(MessageManager.getString("label.output_seq_details"));
498 return maxLineLength;
501 public void createTooltipAnnotationReport(final StringBuilder tip,
502 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
503 FeatureRendererModel fr)
505 int maxWidth = createSequenceAnnotationReport(tip, sequence,
506 showDbRefs, showNpFeats, fr, true);
510 // ? not sure this serves any useful purpose
511 // tip.insert(0, "<table width=350 border=0><tr><td>");
512 // tip.append("</td></tr></table>");