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.SequenceFeature;
25 import jalview.datamodel.SequenceI;
26 import jalview.io.gff.GffConstants;
27 import jalview.util.DBRefUtils;
28 import jalview.util.UrlLink;
30 import java.util.ArrayList;
31 import java.util.List;
35 * generate HTML reports for a sequence
39 public class SequenceAnnotationReport
41 final String linkImageURL;
43 public SequenceAnnotationReport(String linkImageURL)
45 this.linkImageURL = linkImageURL;
49 * Append text for the list of features to the tooltip
56 public void appendFeatures(final StringBuffer tooltipText2, int rpos,
57 List<SequenceFeature> features, Map<String, float[][]> minmax)
61 for (SequenceFeature feature : features)
63 appendFeature(tooltipText2, rpos, minmax, feature);
69 * Appends text for one sequence feature to the string buffer
74 * {{min, max}, {min, max}} positional and non-positional feature
75 * scores for this type
78 void appendFeature(final StringBuffer sb, int rpos,
79 Map<String, float[][]> minmax, SequenceFeature feature)
81 if ("disulfide bond".equals(feature.getType()))
83 if (feature.getBegin() == rpos || feature.getEnd() == rpos)
89 sb.append("disulfide bond ").append(feature.getBegin()).append(":")
90 .append(feature.getEnd());
99 // TODO: remove this hack to display link only features
100 boolean linkOnly = feature.getValue("linkonly") != null;
103 sb.append(feature.getType()).append(" ");
106 // we are marking a positional feature
107 sb.append(feature.begin);
109 if (feature.begin != feature.end)
111 sb.append(" " + feature.end);
114 if (feature.getDescription() != null
115 && !feature.description.equals(feature.getType()))
117 String tmpString = feature.getDescription();
118 String tmp2up = tmpString.toUpperCase();
119 final int startTag = tmp2up.indexOf("<HTML>");
122 tmpString = tmpString.substring(startTag + 6);
123 tmp2up = tmp2up.substring(startTag + 6);
125 // TODO strips off </body> but not <body> - is that intended?
126 int endTag = tmp2up.indexOf("</BODY>");
129 tmpString = tmpString.substring(0, endTag);
130 tmp2up = tmp2up.substring(0, endTag);
132 endTag = tmp2up.indexOf("</HTML>");
135 tmpString = tmpString.substring(0, endTag);
140 sb.append("; ").append(tmpString);
144 if (tmpString.indexOf("<") > -1
145 || tmpString.indexOf(">") > -1)
147 // The description does not specify html is to
148 // be used, so we must remove < > symbols
149 tmpString = tmpString.replaceAll("<", "<");
150 tmpString = tmpString.replaceAll(">", ">");
151 sb.append("; ").append(tmpString);
155 sb.append("; ").append(tmpString);
161 * score should be shown if there is one, and min != max
162 * for this feature type (e.g. not all 0)
164 if (!Float.isNaN(feature.getScore()))
166 float[][] rng = (minmax == null) ? null : minmax.get(feature
168 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
170 sb.append(" Score=").append(
171 String.valueOf(feature.getScore()));
174 String status = (String) feature.getValue("status");
175 if (status != null && status.length() > 0)
177 sb.append("; (").append(status).append(")");
179 String clinSig = (String) feature
180 .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
183 sb.append("; ").append(clinSig);
187 appendLinks(sb, feature);
191 * Format and appends any hyperlinks for the sequence feature to the string
197 void appendLinks(final StringBuffer sb, SequenceFeature feature)
199 if (feature.links != null)
201 if (linkImageURL != null)
203 sb.append(" <img src=\"" + linkImageURL + "\">");
207 for (String urlstring : feature.links)
211 for (String[] urllink : createLinksFrom(null, urlstring))
213 sb.append("<br/> <a href=\""
218 + (urllink[0].toLowerCase().equals(
219 urllink[1].toLowerCase()) ? urllink[0]
220 : (urllink[0] + ":" + urllink[1]))
223 } catch (Exception x)
225 System.err.println("problem when creating links from "
239 * @return String[][] { String[] { link target, link label, dynamic component
240 * inserted (if any), url }}
242 String[][] createLinksFrom(SequenceI seq, String link)
244 List<String[]> urlSets = new ArrayList<String[]>();
245 List<String> uniques = new ArrayList<String>();
246 UrlLink urlLink = new UrlLink(link);
247 if (!urlLink.isValid())
249 System.err.println(urlLink.getInvalidMessage());
252 if (seq != null && urlLink.isDynamic())
254 urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
258 String target = urlLink.getTarget();
259 String label = urlLink.getLabel();
260 String unq = label + "|" + urlLink.getUrl_prefix();
261 if (!uniques.contains(unq))
264 urlSets.add(new String[] { target, label, null,
265 urlLink.getUrl_prefix() });
269 return urlSets.toArray(new String[][] {});
273 * Formats and returns a list of dynamic href links
279 List<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
280 List<String> uniques)
282 List<String[]> result = new ArrayList<String[]>();
283 final String target = urlLink.getTarget();
284 final String label = urlLink.getLabel();
286 // collect matching db-refs
287 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
288 new String[] { target });
289 // collect id string too
290 String id = seq.getName();
291 String descr = seq.getDescription();
292 if (descr != null && descr.length() < 1)
298 for (int r = 0; r < dbr.length; r++)
300 if (id != null && dbr[r].getAccessionId().equals(id))
302 // suppress duplicate link creation for the bare sequence ID
303 // string with this link
306 // create Bare ID link for this URL
307 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
310 for (int u = 0; u < urls.length; u += 2)
312 String unq = urls[u] + "|" + urls[u + 1];
313 if (!uniques.contains(unq))
315 result.add(new String[] { target, label, urls[u],
325 // create Bare ID link for this URL
326 String[] urls = urlLink.makeUrls(id, true);
329 for (int u = 0; u < urls.length; u += 2)
331 String unq = urls[u] + "|" + urls[u + 1];
332 if (!uniques.contains(unq))
334 result.add(new String[] { target, label, urls[u],
341 if (descr != null && urlLink.getRegexReplace() != null)
343 // create link for this URL from description only if regex matches
344 String[] urls = urlLink.makeUrls(descr, true);
347 for (int u = 0; u < urls.length; u += 2)
349 String unq = urls[u] + "|" + urls[u + 1];
350 if (!uniques.contains(unq))
352 result.add(new String[] { target, label, urls[u],
362 public void createSequenceAnnotationReport(final StringBuffer tip,
363 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
364 Map<String, float[][]> minmax)
366 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
370 public void createSequenceAnnotationReport(final StringBuffer tip,
371 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
372 boolean tableWrap, Map<String, float[][]> minmax)
378 if (sequence.getDescription() != null)
380 tmp = sequence.getDescription();
381 tip.append("<br>" + tmp);
382 maxWidth = Math.max(maxWidth, tmp.length());
384 SequenceI ds = sequence;
385 while (ds.getDatasetSequence() != null)
387 ds = ds.getDatasetSequence();
389 DBRefEntry[] dbrefs = ds.getDBRefs();
390 if (showDbRefs && dbrefs != null)
392 for (int i = 0; i < dbrefs.length; i++)
395 tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
397 maxWidth = Math.max(maxWidth, tmp.length());
401 // ADD NON POSITIONAL SEQUENCE INFO
402 SequenceFeature[] features = sequence.getSequenceFeatures();
403 if (showNpFeats && features != null)
405 for (int i = 0; i < features.length; i++)
407 if (features[i].begin == 0 && features[i].end == 0)
409 int sz = -tip.length();
410 List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
411 tfeat.add(features[i]);
412 appendFeatures(tip, 0, tfeat, minmax);
414 maxWidth = Math.max(maxWidth, sz);
419 if (tableWrap && maxWidth > 60)
421 tip.insert(0, "<table width=350 border=0><tr><td><i>");
422 tip.append("</i></td></tr></table>");