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 || tmpString.indexOf(">") > -1)
146 // The description does not specify html is to
147 // be used, so we must remove < > symbols
148 tmpString = tmpString.replaceAll("<", "<");
149 tmpString = tmpString.replaceAll(">", ">");
150 sb.append("; ").append(tmpString);
154 sb.append("; ").append(tmpString);
160 * score should be shown if there is one, and min != max
161 * for this feature type (e.g. not all 0)
163 if (!Float.isNaN(feature.getScore()))
165 float[][] rng = (minmax == null) ? null : minmax.get(feature
167 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
169 sb.append(" Score=").append(String.valueOf(feature.getScore()));
172 String status = (String) feature.getValue("status");
173 if (status != null && status.length() > 0)
175 sb.append("; (").append(status).append(")");
177 String clinSig = (String) feature
178 .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
181 sb.append("; ").append(clinSig);
185 appendLinks(sb, feature);
189 * Format and appends any hyperlinks for the sequence feature to the string
195 void appendLinks(final StringBuffer sb, SequenceFeature feature)
197 if (feature.links != null)
199 if (linkImageURL != null)
201 sb.append(" <img src=\"" + linkImageURL + "\">");
205 for (String urlstring : feature.links)
209 for (String[] urllink : createLinksFrom(null, urlstring))
211 sb.append("<br/> <a href=\""
216 + (urllink[0].toLowerCase().equals(
217 urllink[1].toLowerCase()) ? urllink[0]
218 : (urllink[0] + ":" + urllink[1]))
221 } catch (Exception x)
223 System.err.println("problem when creating links from "
237 * @return String[][] { String[] { link target, link label, dynamic component
238 * inserted (if any), url }}
240 String[][] createLinksFrom(SequenceI seq, String link)
242 List<String[]> urlSets = new ArrayList<String[]>();
243 List<String> uniques = new ArrayList<String>();
244 UrlLink urlLink = new UrlLink(link);
245 if (!urlLink.isValid())
247 System.err.println(urlLink.getInvalidMessage());
250 if (seq != null && urlLink.isDynamic())
252 urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
256 String target = urlLink.getTarget();
257 String label = urlLink.getLabel();
258 String unq = label + "|" + urlLink.getUrl_prefix();
259 if (!uniques.contains(unq))
262 urlSets.add(new String[] { target, label, null,
263 urlLink.getUrl_prefix() });
267 return urlSets.toArray(new String[][] {});
271 * Formats and returns a list of dynamic href links
277 List<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
278 List<String> uniques)
280 List<String[]> result = new ArrayList<String[]>();
281 final String target = urlLink.getTarget();
282 final String label = urlLink.getLabel();
284 // collect matching db-refs
285 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
286 new String[] { target });
287 // collect id string too
288 String id = seq.getName();
289 String descr = seq.getDescription();
290 if (descr != null && descr.length() < 1)
296 for (int r = 0; r < dbr.length; r++)
298 if (id != null && dbr[r].getAccessionId().equals(id))
300 // suppress duplicate link creation for the bare sequence ID
301 // string with this link
304 // create Bare ID link for this URL
305 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
308 for (int u = 0; u < urls.length; u += 2)
310 String unq = urls[u] + "|" + urls[u + 1];
311 if (!uniques.contains(unq))
313 result.add(new String[] { target, label, urls[u], urls[u + 1] });
322 // create Bare ID link for this URL
323 String[] urls = urlLink.makeUrls(id, true);
326 for (int u = 0; u < urls.length; u += 2)
328 String unq = urls[u] + "|" + urls[u + 1];
329 if (!uniques.contains(unq))
331 result.add(new String[] { target, label, urls[u], urls[u + 1] });
337 if (descr != null && urlLink.getRegexReplace() != null)
339 // create link for this URL from description only if regex matches
340 String[] urls = urlLink.makeUrls(descr, true);
343 for (int u = 0; u < urls.length; u += 2)
345 String unq = urls[u] + "|" + urls[u + 1];
346 if (!uniques.contains(unq))
348 result.add(new String[] { target, label, urls[u], urls[u + 1] });
357 public void createSequenceAnnotationReport(final StringBuffer tip,
358 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
359 Map<String, float[][]> minmax)
361 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
365 public void createSequenceAnnotationReport(final StringBuffer tip,
366 SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
367 boolean tableWrap, Map<String, float[][]> minmax)
373 if (sequence.getDescription() != null)
375 tmp = sequence.getDescription();
376 tip.append("<br>" + tmp);
377 maxWidth = Math.max(maxWidth, tmp.length());
379 SequenceI ds = sequence;
380 while (ds.getDatasetSequence() != null)
382 ds = ds.getDatasetSequence();
384 DBRefEntry[] dbrefs = ds.getDBRefs();
385 if (showDbRefs && dbrefs != null)
387 for (int i = 0; i < dbrefs.length; i++)
390 tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
392 maxWidth = Math.max(maxWidth, tmp.length());
396 // ADD NON POSITIONAL SEQUENCE INFO
397 SequenceFeature[] features = sequence.getSequenceFeatures();
398 if (showNpFeats && features != null)
400 for (int i = 0; i < features.length; i++)
402 if (features[i].begin == 0 && features[i].end == 0)
404 int sz = -tip.length();
405 List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
406 tfeat.add(features[i]);
407 appendFeatures(tip, 0, tfeat, minmax);
409 maxWidth = Math.max(maxWidth, sz);
414 if (tableWrap && maxWidth > 60)
416 tip.insert(0, "<table width=350 border=0><tr><td><i>");
417 tip.append("</i></td></tr></table>");