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.SequenceFeature;
28 import jalview.datamodel.SequenceI;
29 import jalview.util.MessageManager;
30 import jalview.util.StringUtils;
31 import jalview.util.UrlLink;
32 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
34 import java.util.Arrays;
35 import java.util.Collection;
36 import java.util.Comparator;
37 import java.util.LinkedHashMap;
38 import java.util.List;
42 * generate HTML reports for a sequence
46 public class SequenceAnnotationReport
48 private static final String COMMA = ",";
50 private static final String ELLIPSIS = "...";
52 private static final int MAX_REFS_PER_SOURCE = 4;
54 private static final int MAX_SOURCES = 40;
56 // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
58 final String linkImageURL;
61 * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
62 * with 'Primary' sources placed before others, and 'chromosome' first of all
64 private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
68 public int compare(DBRefEntry ref1, DBRefEntry ref2)
70 if (ref1 instanceof GeneLociI)
74 if (ref2 instanceof GeneLociI)
78 String s1 = ref1.getSource();
79 String s2 = ref2.getSource();
80 boolean s1Primary = DBRefSource.isPrimarySource(s1);
81 boolean s2Primary = DBRefSource.isPrimarySource(s2);
82 if (s1Primary && !s2Primary)
86 if (!s1Primary && s2Primary)
90 int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
91 .compareToIgnoreCase(s2));
94 String a1 = ref1.getAccessionId();
95 String a2 = ref2.getAccessionId();
96 comp = a1 == null ? -1 : (a2 == null ? 1 : a1
97 .compareToIgnoreCase(a2));
102 // private boolean isPrimarySource(String source)
104 // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
106 // for (String s : primary)
108 // if (source.equals(s))
118 public SequenceAnnotationReport(String linkURL)
120 this.linkImageURL = linkURL;
124 * Append text for the list of features to the tooltip
131 public void appendFeatures(final StringBuilder sb, int rpos,
132 List<SequenceFeature> features, FeatureRendererModel fr)
134 if (features != null)
136 for (SequenceFeature feature : features)
138 appendFeature(sb, rpos, fr, feature);
144 * Appends the feature at rpos to the given buffer
151 void appendFeature(final StringBuilder sb, int rpos,
152 FeatureRendererModel fr, SequenceFeature feature)
154 if (feature.isContactFeature())
156 if (feature.getBegin() == rpos || feature.getEnd() == rpos)
162 sb.append(feature.getType()).append(" ").append(feature.getBegin())
163 .append(":").append(feature.getEnd());
172 // TODO: remove this hack to display link only features
173 boolean linkOnly = feature.getValue("linkonly") != null;
176 sb.append(feature.getType()).append(" ");
179 // we are marking a positional feature
180 sb.append(feature.begin);
182 if (feature.begin != feature.end)
184 sb.append(" ").append(feature.end);
187 String description = feature.getDescription();
188 if (description != null && !description.equals(feature.getType()))
190 description = StringUtils.stripHtmlTags(description);
191 sb.append("; ").append(description);
194 if (showScore(feature, fr))
196 sb.append(" Score=").append(String.valueOf(feature.getScore()));
198 String status = (String) feature.getValue("status");
199 if (status != null && status.length() > 0)
201 sb.append("; (").append(status).append(")");
205 * add attribute value if coloured by attribute
209 FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
210 if (fc != null && fc.isColourByAttribute())
212 String[] attName = fc.getAttributeName();
213 String attVal = feature.getValueAsString(attName);
216 sb.append("; ").append(String.join(":", attName)).append("=")
225 * Answers true if score should be shown, else false. Score is shown if it is
226 * not NaN, and the feature type has a non-trivial min-max score range
228 boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
230 if (Float.isNaN(feature.getScore()))
238 float[][] minMax = fr.getMinMax().get(feature.getType());
241 * minMax[0] is the [min, max] score range for positional features
243 if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
251 * Format and appends any hyperlinks for the sequence feature to the string
257 void appendLinks(final StringBuffer sb, SequenceFeature feature)
259 if (feature.links != null)
261 if (linkImageURL != null)
263 sb.append(" <img src=\"" + linkImageURL + "\">");
267 for (String urlstring : feature.links)
271 for (List<String> urllink : createLinksFrom(null, urlstring))
273 sb.append("<br/> <a href=\""
278 + (urllink.get(0).toLowerCase()
279 .equals(urllink.get(1).toLowerCase()) ? urllink
280 .get(0) : (urllink.get(0) + ":" + urllink
281 .get(1))) + "</a></br>");
283 } catch (Exception x)
285 System.err.println("problem when creating links from "
299 * @return Collection< List<String> > { List<String> { link target, link
300 * label, dynamic component inserted (if any), url }}
302 Collection<List<String>> createLinksFrom(SequenceI seq, String link)
304 Map<String, List<String>> urlSets = new LinkedHashMap<>();
305 UrlLink urlLink = new UrlLink(link);
306 if (!urlLink.isValid())
308 System.err.println(urlLink.getInvalidMessage());
312 urlLink.createLinksFromSeq(seq, urlSets);
314 return urlSets.values();
317 public void createSequenceAnnotationReport(final StringBuilder tip,
318 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
319 FeatureRendererModel fr)
321 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
326 * Builds an html formatted report of sequence details and appends it to the
330 * buffer to append report to
332 * the sequence the report is for
334 * whether to include database references for the sequence
336 * whether to include non-positional sequence features
341 int createSequenceAnnotationReport(final StringBuilder sb,
342 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
343 FeatureRendererModel fr, boolean summary)
349 if (sequence.getDescription() != null)
351 tmp = sequence.getDescription();
352 sb.append("<br>").append(tmp);
353 maxWidth = Math.max(maxWidth, tmp.length());
355 SequenceI ds = sequence;
356 while (ds.getDatasetSequence() != null)
358 ds = ds.getDatasetSequence();
363 maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
367 * add non-positional features if wanted
371 for (SequenceFeature sf : sequence.getFeatures()
372 .getNonPositionalFeatures())
374 int sz = -sb.length();
375 appendFeature(sb, 0, fr, sf);
377 maxWidth = Math.max(maxWidth, sz);
385 * A helper method that appends any DBRefs, returning the maximum line length
393 protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
396 List<DBRefEntry> dbrefs = ds.getDBRefs();
402 // note this sorts the refs held on the sequence!
403 dbrefs.sort(comparator);
404 boolean ellipsis = false;
405 String source = null;
406 String lastSource = null;
407 int countForSource = 0;
409 boolean moreSources = false;
410 int maxLineLength = 0;
413 for (DBRefEntry ref : dbrefs)
415 source = ref.getSource();
421 boolean sourceChanged = !source.equals(lastSource);
428 if (sourceCount > MAX_SOURCES && summary)
436 if (countForSource == 1 || !summary)
440 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
442 String accessionId = ref.getAccessionId();
443 lineLength += accessionId.length() + 1;
444 if (countForSource > 1 && summary)
446 sb.append(", ").append(accessionId);
451 sb.append(source).append(" ").append(accessionId);
452 lineLength += source.length();
454 maxLineLength = Math.max(maxLineLength, lineLength);
456 if (countForSource == MAX_REFS_PER_SOURCE && summary)
458 sb.append(COMMA).append(ELLIPSIS);
464 sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
469 sb.append(MessageManager.getString("label.output_seq_details"));
473 return maxLineLength;
476 public void createTooltipAnnotationReport(final StringBuilder tip,
477 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
478 FeatureRendererModel fr)
480 int maxWidth = createSequenceAnnotationReport(tip, sequence,
481 showDbRefs, showNpFeats, fr, true);
485 // ? not sure this serves any useful purpose
486 // tip.insert(0, "<table width=350 border=0><tr><td>");
487 // tip.append("</td></tr></table>");