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 private static final String[][] PRIMARY_SOURCES = new String[][] {
58 DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
59 DBRefSource.PROTEINDBS };
61 final String linkImageURL;
64 * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
65 * with 'Primary' sources placed before others, and 'chromosome' first of all
67 private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
71 public int compare(DBRefEntry ref1, DBRefEntry ref2)
73 if (ref1 instanceof GeneLociI)
77 if (ref2 instanceof GeneLociI)
81 String s1 = ref1.getSource();
82 String s2 = ref2.getSource();
83 boolean s1Primary = isPrimarySource(s1);
84 boolean s2Primary = isPrimarySource(s2);
85 if (s1Primary && !s2Primary)
89 if (!s1Primary && s2Primary)
93 int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
94 .compareToIgnoreCase(s2));
97 String a1 = ref1.getAccessionId();
98 String a2 = ref2.getAccessionId();
99 comp = a1 == null ? -1 : (a2 == null ? 1 : a1
100 .compareToIgnoreCase(a2));
105 private boolean isPrimarySource(String source)
107 for (String[] primary : PRIMARY_SOURCES)
109 for (String s : primary)
111 if (source.equals(s))
121 public SequenceAnnotationReport(String linkURL)
123 this.linkImageURL = linkURL;
127 * Append text for the list of features to the tooltip
134 public void appendFeatures(final StringBuilder sb, int residuePos,
135 List<SequenceFeature> features, FeatureRendererModel fr)
137 for (SequenceFeature feature : features)
139 appendFeature(sb, residuePos, fr, feature, null);
144 * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
151 public void appendFeatures(StringBuilder sb, int residuePos,
152 MappedFeatures mf, FeatureRendererModel fr)
154 for (SequenceFeature feature : mf.features)
156 appendFeature(sb, residuePos, fr, feature, mf);
161 * Appends the feature at rpos to the given buffer
168 void appendFeature(final StringBuilder sb, int rpos,
169 FeatureRendererModel fr, SequenceFeature feature,
172 if (feature.isContactFeature())
174 if (feature.getBegin() == rpos || feature.getEnd() == rpos)
180 sb.append(feature.getType()).append(" ").append(feature.getBegin())
181 .append(":").append(feature.getEnd());
190 // TODO: remove this hack to display link only features
191 boolean linkOnly = feature.getValue("linkonly") != null;
194 sb.append(feature.getType()).append(" ");
197 // we are marking a positional feature
198 sb.append(feature.begin);
200 if (feature.begin != feature.end)
202 sb.append(" ").append(feature.end);
205 String description = feature.getDescription();
206 if (description != null && !description.equals(feature.getType()))
208 description = StringUtils.stripHtmlTags(description);
209 sb.append("; ").append(description);
212 if (showScore(feature, fr))
214 sb.append(" Score=").append(String.valueOf(feature.getScore()));
216 String status = (String) feature.getValue("status");
217 if (status != null && status.length() > 0)
219 sb.append("; (").append(status).append(")");
223 * add attribute value if coloured by attribute
227 FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
228 if (fc != null && fc.isColourByAttribute())
230 String[] attName = fc.getAttributeName();
231 String attVal = feature.getValueAsString(attName);
234 sb.append("; ").append(String.join(":", attName)).append("=")
242 String variants = mf.findProteinVariants(feature);
243 if (!variants.isEmpty())
245 sb.append(" ").append(variants);
252 * Answers true if score should be shown, else false. Score is shown if it is
253 * not NaN, and the feature type has a non-trivial min-max score range
255 boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
257 if (Float.isNaN(feature.getScore()))
265 float[][] minMax = fr.getMinMax().get(feature.getType());
268 * minMax[0] is the [min, max] score range for positional features
270 if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
278 * Format and appends any hyperlinks for the sequence feature to the string
284 void appendLinks(final StringBuffer sb, SequenceFeature feature)
286 if (feature.links != null)
288 if (linkImageURL != null)
290 sb.append(" <img src=\"" + linkImageURL + "\">");
294 for (String urlstring : feature.links)
298 for (List<String> urllink : createLinksFrom(null, urlstring))
300 sb.append("<br/> <a href=\""
305 + (urllink.get(0).toLowerCase()
306 .equals(urllink.get(1).toLowerCase()) ? urllink
307 .get(0) : (urllink.get(0) + ":" + urllink
308 .get(1))) + "</a></br>");
310 } catch (Exception x)
312 System.err.println("problem when creating links from "
326 * @return Collection< List<String> > { List<String> { link target, link
327 * label, dynamic component inserted (if any), url }}
329 Collection<List<String>> createLinksFrom(SequenceI seq, String link)
331 Map<String, List<String>> urlSets = new LinkedHashMap<>();
332 UrlLink urlLink = new UrlLink(link);
333 if (!urlLink.isValid())
335 System.err.println(urlLink.getInvalidMessage());
339 urlLink.createLinksFromSeq(seq, urlSets);
341 return urlSets.values();
344 public void createSequenceAnnotationReport(final StringBuilder tip,
345 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
346 FeatureRendererModel fr)
348 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
353 * Builds an html formatted report of sequence details and appends it to the
357 * buffer to append report to
359 * the sequence the report is for
361 * whether to include database references for the sequence
363 * whether to include non-positional sequence features
368 int createSequenceAnnotationReport(final StringBuilder sb,
369 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
370 FeatureRendererModel fr, boolean summary)
376 if (sequence.getDescription() != null)
378 tmp = sequence.getDescription();
379 sb.append("<br>").append(tmp);
380 maxWidth = Math.max(maxWidth, tmp.length());
382 SequenceI ds = sequence;
383 while (ds.getDatasetSequence() != null)
385 ds = ds.getDatasetSequence();
390 maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
394 * add non-positional features if wanted
398 for (SequenceFeature sf : sequence.getFeatures()
399 .getNonPositionalFeatures())
401 int sz = -sb.length();
402 appendFeature(sb, 0, fr, sf, null);
404 maxWidth = Math.max(maxWidth, sz);
412 * A helper method that appends any DBRefs, returning the maximum line length
420 protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
423 DBRefEntry[] dbrefs = ds.getDBRefs();
429 // note this sorts the refs held on the sequence!
430 Arrays.sort(dbrefs, comparator);
431 boolean ellipsis = false;
432 String source = null;
433 String lastSource = null;
434 int countForSource = 0;
436 boolean moreSources = false;
437 int maxLineLength = 0;
440 for (DBRefEntry ref : dbrefs)
442 source = ref.getSource();
448 boolean sourceChanged = !source.equals(lastSource);
455 if (sourceCount > MAX_SOURCES && summary)
463 if (countForSource == 1 || !summary)
467 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
469 String accessionId = ref.getAccessionId();
470 lineLength += accessionId.length() + 1;
471 if (countForSource > 1 && summary)
473 sb.append(", ").append(accessionId);
478 sb.append(source).append(" ").append(accessionId);
479 lineLength += source.length();
481 maxLineLength = Math.max(maxLineLength, lineLength);
483 if (countForSource == MAX_REFS_PER_SOURCE && summary)
485 sb.append(COMMA).append(ELLIPSIS);
491 sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
496 sb.append(MessageManager.getString("label.output_seq_details"));
500 return maxLineLength;
503 public void createTooltipAnnotationReport(final StringBuilder tip,
504 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
505 FeatureRendererModel fr)
507 int maxWidth = createSequenceAnnotationReport(tip, sequence,
508 showDbRefs, showNpFeats, fr, true);
512 // ? not sure this serves any useful purpose
513 // tip.insert(0, "<table width=350 border=0><tr><td>");
514 // tip.append("</td></tr></table>");