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.StringUtils;
30 import jalview.util.UrlLink;
32 import java.util.Arrays;
33 import java.util.Collection;
34 import java.util.Comparator;
35 import java.util.LinkedHashMap;
36 import java.util.List;
40 * generate HTML reports for a sequence
44 public class SequenceAnnotationReport
46 private static final String COMMA = ",";
48 private static final String ELLIPSIS = "...";
50 private static final int MAX_REFS_PER_SOURCE = 4;
52 private static final int MAX_SOURCES = 40;
54 private static final String[][] PRIMARY_SOURCES = new String[][] {
55 DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
56 DBRefSource.PROTEINDBS };
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.isChromosome())
74 if (ref2.isChromosome())
78 String s1 = ref1.getSource();
79 String s2 = ref2.getSource();
80 boolean s1Primary = isPrimarySource(s1);
81 boolean s2Primary = isPrimarySource(s2);
82 if (s1Primary && !s2Primary)
86 if (!s1Primary && s2Primary)
90 int comp = s1 == null ? -1
91 : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
94 String a1 = ref1.getAccessionId();
95 String a2 = ref2.getAccessionId();
96 comp = a1 == null ? -1
97 : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
102 private boolean isPrimarySource(String source)
104 for (String[] primary : PRIMARY_SOURCES)
106 for (String s : primary)
108 if (source.equals(s))
118 public SequenceAnnotationReport(String linkImageURL)
120 this.linkImageURL = linkImageURL;
124 * Append text for the list of features to the tooltip
131 public void appendFeatures(final StringBuilder sb, int rpos,
132 List<SequenceFeature> features, Map<String, float[][]> minmax)
134 if (features != null)
136 for (SequenceFeature feature : features)
138 appendFeature(sb, rpos, minmax, feature);
144 * Appends the feature at rpos to the given buffer
151 void appendFeature(final StringBuilder sb, int rpos,
152 Map<String, float[][]> minmax, 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);
193 // check score should be shown
194 if (!Float.isNaN(feature.getScore()))
196 float[][] rng = (minmax == null) ? null
197 : minmax.get(feature.getType());
198 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
200 sb.append(" Score=").append(String.valueOf(feature.getScore()));
203 String status = (String) feature.getValue("status");
204 if (status != null && status.length() > 0)
206 sb.append("; (").append(status).append(")");
208 String clinSig = (String) feature
209 .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
212 sb.append("; ").append(clinSig);
219 * Format and appends any hyperlinks for the sequence feature to the string
225 void appendLinks(final StringBuffer sb, SequenceFeature feature)
227 if (feature.links != null)
229 if (linkImageURL != null)
231 sb.append(" <img src=\"" + linkImageURL + "\">");
235 for (String urlstring : feature.links)
239 for (List<String> urllink : createLinksFrom(null, urlstring))
241 sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
242 + urllink.get(0) + "\">"
243 + (urllink.get(0).toLowerCase()
244 .equals(urllink.get(1).toLowerCase())
246 : (urllink.get(0) + ":"
250 } catch (Exception x)
253 "problem when creating links from " + urlstring);
266 * @return Collection< List<String> > { List<String> { link target, link
267 * label, dynamic component inserted (if any), url }}
269 Collection<List<String>> createLinksFrom(SequenceI seq, String link)
271 Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
272 UrlLink urlLink = new UrlLink(link);
273 if (!urlLink.isValid())
275 System.err.println(urlLink.getInvalidMessage());
279 urlLink.createLinksFromSeq(seq, urlSets);
281 return urlSets.values();
284 public void createSequenceAnnotationReport(final StringBuilder tip,
285 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
286 Map<String, float[][]> minmax)
288 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
293 * Builds an html formatted report of sequence details and appends it to the
297 * buffer to append report to
299 * the sequence the report is for
301 * whether to include database references for the sequence
303 * whether to include non-positional sequence features
308 int createSequenceAnnotationReport(final StringBuilder sb,
309 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
310 Map<String, float[][]> minmax, boolean summary)
316 if (sequence.getDescription() != null)
318 tmp = sequence.getDescription();
319 sb.append("<br>").append(tmp);
320 maxWidth = Math.max(maxWidth, tmp.length());
322 SequenceI ds = sequence;
323 while (ds.getDatasetSequence() != null)
325 ds = ds.getDatasetSequence();
330 maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
334 * add non-positional features if wanted
338 for (SequenceFeature sf : sequence.getFeatures()
339 .getNonPositionalFeatures())
341 int sz = -sb.length();
342 appendFeature(sb, 0, minmax, sf);
344 maxWidth = Math.max(maxWidth, sz);
352 * A helper method that appends any DBRefs, returning the maximum line length
360 protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
363 DBRefEntry[] dbrefs = ds.getDBRefs();
369 // note this sorts the refs held on the sequence!
370 Arrays.sort(dbrefs, comparator);
371 boolean ellipsis = false;
372 String source = null;
373 String lastSource = null;
374 int countForSource = 0;
376 boolean moreSources = false;
377 int maxLineLength = 0;
380 for (DBRefEntry ref : dbrefs)
382 source = ref.getSource();
388 boolean sourceChanged = !source.equals(lastSource);
395 if (sourceCount > MAX_SOURCES && summary)
403 if (countForSource == 1 || !summary)
407 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
409 String accessionId = ref.getAccessionId();
410 lineLength += accessionId.length() + 1;
411 if (countForSource > 1 && summary)
413 sb.append(", ").append(accessionId);
418 sb.append(source).append(" ").append(accessionId);
419 lineLength += source.length();
421 maxLineLength = Math.max(maxLineLength, lineLength);
423 if (countForSource == MAX_REFS_PER_SOURCE && summary)
425 sb.append(COMMA).append(ELLIPSIS);
431 sb.append("<br>").append(source)
432 .append(COMMA).append(ELLIPSIS);
437 sb.append(MessageManager.getString("label.output_seq_details"));
441 return maxLineLength;
444 public void createTooltipAnnotationReport(final StringBuilder tip,
445 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
446 Map<String, float[][]> minmax)
448 int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
449 showNpFeats, minmax, true);
453 // ? not sure this serves any useful purpose
454 // tip.insert(0, "<table width=350 border=0><tr><td>");
455 // tip.append("</td></tr></table>");