*/
package jalview.io;
+import java.util.ArrayList;
+
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import jalview.api.FeatureColourI;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
* if this is a virtual features, convert begin/end to the
* coordinates of the sequence it is mapped to
*/
- int[] beginRange = null;
- int[] endRange = null;
+ int[] beginRange = null; // feature start in local coordinates
+ int[] endRange = null; // feature end in local coordinates
if (mf != null)
{
- beginRange = mf.getMappedPositions(begin, begin);
- endRange = mf.getMappedPositions(end, end);
+ if (feature.isContactFeature())
+ {
+ /*
+ * map start and end points individually
+ */
+ beginRange = mf.getMappedPositions(begin, begin);
+ endRange = begin == end ? beginRange
+ : mf.getMappedPositions(end, end);
+ }
+ else
+ {
+ /*
+ * map the feature extent
+ */
+ beginRange = mf.getMappedPositions(begin, end);
+ endRange = beginRange;
+ }
if (beginRange == null || endRange == null)
{
// something went wrong
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
- int linkindex = description.toLowerCase().indexOf("<a ");
+ int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
boolean hasLink = linkindex > -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
- if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ if (
+ // BH suggestion maxlength == 0 &&
+ description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
{
description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ ELLIPSIS;
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
+ sb.append("<br> <a href=\""
+ urllink.get(3)
+ "\" target=\""
+ urllink.get(0)
+ "\">"
- + (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
+ + (urllink.get(0).toLowerCase(Locale.ROOT)
+ .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
- + "</a><br/>");
+ + "</a><br>");
}
} catch (Exception x)
{
sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+ sb.append("\n");
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
+
+ /*
+ * add any annotation scores
+ */
+ AlignmentAnnotation[] anns = ds.getAnnotation();
+ if (anns!=null && anns.length>0) {
+ boolean first=true;
+ for (int i = 0; anns != null && i < anns.length; i++)
+ {
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
+ {
+ if (first) {
+ sb.append("<br>").append("Annotation Scores<br>");
+ first=false;
+ }
+ sb.append("<br>").append(aa.label).append(": ")
+ .append(aa.getScore());
+ }
+ }
+ }
if (showDbRefs)
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
}
+ sb.append("\n");
/*
* add non-positional features if wanted
maxWidth = Math.max(maxWidth, sz);
}
}
+ if (sequence.getAnnotation("Search Scores") != null)
+ {
+ sb.append("<br>");
+ String eValue = " E-Value: "
+ + sequence.getAnnotation("Search Scores")[0].getEValue();
+ String bitScore = " Bit Score: "
+ + sequence.getAnnotation("Search Scores")[0].getBitScore();
+ sb.append(eValue);
+ sb.append("<br>");
+ sb.append(bitScore);
+ maxWidth = Math.max(maxWidth, eValue.length());
+ maxWidth = Math.max(maxWidth, bitScore.length());
+ sb.append("<br>");
+ }
sb.append("</i>");
return maxWidth;
}
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- List<DBRefEntry> dbrefs = ds.getDBRefs();
- if (dbrefs == null)
+ List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
+
+ if (dbrefset == null)
{
return 0;
}
+ // PATCH for JAL-3980 defensive copy
+
+ dbrefs = new ArrayList<DBRefEntry>();
+
+ dbrefs.addAll(dbrefset);
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("<br/>");
+ sb.append("<br/>\n");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
lineLength += accessionId.length() + 1;
if (countForSource > 1 && summary)
{
- sb.append(", ").append(accessionId);
+ sb.append(",\n ").append(accessionId);
lineLength++;
}
else
}
if (moreSources)
{
- sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
+ sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("<br/>(");
+ sb.append("<br/>\n(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}