final String linkImageURL;
/*
- * Comparator to order DBRefEntry by Source + accession id (case-insensitive)
+ * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
+ * with 'Primary' sources placed before others
*/
private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
{
{
return 1;
}
- int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
- .compareToIgnoreCase(s2));
+ int comp = s1 == null ? -1
+ : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
if (comp == 0)
{
String a1 = ref1.getAccessionId();
String a2 = ref2.getAccessionId();
- comp = a1 == null ? -1 : (a2 == null ? 1 : a1
- .compareToIgnoreCase(a2));
+ comp = a1 == null ? -1
+ : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
}
return comp;
}
sb.append("<br>");
}
sb.append(feature.getType()).append(" ").append(feature.getBegin())
- .append(":")
- .append(feature.getEnd());
+ .append(":").append(feature.getEnd());
}
}
else
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : minmax.get(feature
- .getType());
+ float[][] rng = (minmax == null) ? null
+ : minmax.get(feature.getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
sb.append(" Score=").append(String.valueOf(feature.getScore()));
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
- + urllink.get(3)
- + "\" target=\""
- + urllink.get(0)
- + "\">"
+ sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+ + urllink.get(0) + "\">"
+ (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
- .get(0) : (urllink.get(0) + ":" + urllink
- .get(1)))
+ .equals(urllink.get(1).toLowerCase())
+ ? urllink.get(0)
+ : (urllink.get(0) + ":"
+ + urllink.get(1)))
+ "</a></br>");
}
} catch (Exception x)
{
- System.err.println("problem when creating links from "
- + urlstring);
+ System.err.println(
+ "problem when creating links from " + urlstring);
x.printStackTrace();
}
}
{
ds = ds.getDatasetSequence();
}
+
+ if (showDbRefs)
+ {
+ maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+ }
+
+ /*
+ * add non-positional features if wanted
+ */
+ if (showNpFeats)
+ {
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
+ {
+ int sz = -sb.length();
+ appendFeature(sb, 0, minmax, sf);
+ sz += sb.length();
+ maxWidth = Math.max(maxWidth, sz);
+ }
+ }
+ sb.append("</i>");
+ return maxWidth;
+ }
+
+ /**
+ * A helper method that appends any DBRefs, returning the maximum line length
+ * added
+ *
+ * @param sb
+ * @param ds
+ * @param summary
+ * @return
+ */
+ protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
+ boolean summary)
+ {
DBRefEntry[] dbrefs = ds.getDBRefs();
- if (showDbRefs && dbrefs != null)
+ if (dbrefs == null)
+ {
+ return 0;
+ }
+
+ // note this sorts the refs held on the sequence!
+ Arrays.sort(dbrefs, comparator);
+ boolean ellipsis = false;
+ String source = null;
+ String lastSource = null;
+ int countForSource = 0;
+ int sourceCount = 0;
+ boolean moreSources = false;
+ int maxLineLength = 0;
+ int lineLength = 0;
+
+ for (DBRefEntry ref : dbrefs)
{
- // note this sorts the refs held on the sequence!
- Arrays.sort(dbrefs, comparator);
- boolean ellipsis = false;
- String source = null;
- String lastSource = null;
- int countForSource = 0;
- int sourceCount = 0;
- boolean moreSources = false;
- int lineLength = 0;
-
- for (DBRefEntry ref : dbrefs)
+ source = ref.getSource();
+ if (source == null)
{
- source = ref.getSource();
- if (source == null)
- {
- // shouldn't happen
- continue;
- }
- boolean sourceChanged = !source.equals(lastSource);
- if (sourceChanged)
- {
- lineLength = 0;
- countForSource = 0;
- sourceCount++;
- }
- if (sourceCount > MAX_SOURCES && summary)
- {
- ellipsis = true;
- moreSources = true;
- break;
- }
- lastSource = source;
- countForSource++;
- if (countForSource == 1 || !summary)
- {
- sb.append("<br>");
- }
- if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
- {
- String accessionId = ref.getAccessionId();
- lineLength += accessionId.length() + 1;
- if (countForSource > 1 && summary)
- {
- sb.append(", ").append(accessionId);
- lineLength++;
- }
- else
- {
- sb.append(source).append(" ").append(accessionId);
- lineLength += source.length();
- }
- maxWidth = Math.max(maxWidth, lineLength);
- }
- if (countForSource == MAX_REFS_PER_SOURCE && summary)
- {
- sb.append(COMMA).append(ELLIPSIS);
- ellipsis = true;
- }
+ // shouldn't happen
+ continue;
}
- if (moreSources)
+ boolean sourceChanged = !source.equals(lastSource);
+ if (sourceChanged)
{
- sb.append("<br>").append(ELLIPSIS).append(COMMA).append(source)
- .append(COMMA).append(ELLIPSIS);
+ lineLength = 0;
+ countForSource = 0;
+ sourceCount++;
}
- if (ellipsis)
+ if (sourceCount > MAX_SOURCES && summary)
{
- sb.append("<br>(");
- sb.append(MessageManager.getString("label.output_seq_details"));
- sb.append(")");
+ ellipsis = true;
+ moreSources = true;
+ break;
}
- }
-
- /*
- * add non-positional features if wanted
- */
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (showNpFeats && features != null)
- {
- for (int i = 0; i < features.length; i++)
+ lastSource = source;
+ countForSource++;
+ if (countForSource == 1 || !summary)
+ {
+ sb.append("<br>");
+ }
+ if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
- if (features[i].begin == 0 && features[i].end == 0)
+ String accessionId = ref.getAccessionId();
+ lineLength += accessionId.length() + 1;
+ if (countForSource > 1 && summary)
{
- int sz = -sb.length();
- appendFeature(sb, 0, minmax, features[i]);
- sz += sb.length();
- maxWidth = Math.max(maxWidth, sz);
+ sb.append(", ").append(accessionId);
+ lineLength++;
}
+ else
+ {
+ sb.append(source).append(" ").append(accessionId);
+ lineLength += source.length();
+ }
+ maxLineLength = Math.max(maxLineLength, lineLength);
+ }
+ if (countForSource == MAX_REFS_PER_SOURCE && summary)
+ {
+ sb.append(COMMA).append(ELLIPSIS);
+ ellipsis = true;
}
}
- sb.append("</i>");
- return maxWidth;
+ if (moreSources)
+ {
+ sb.append("<br>").append(source)
+ .append(COMMA).append(ELLIPSIS);
+ }
+ if (ellipsis)
+ {
+ sb.append("<br>(");
+ sb.append(MessageManager.getString("label.output_seq_details"));
+ sb.append(")");
+ }
+
+ return maxLineLength;
}
public void createTooltipAnnotationReport(final StringBuilder tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
Map<String, float[][]> minmax)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, minmax, true);
+ int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+ showNpFeats, minmax, true);
if (maxWidth > 60)
{
git://source.jalview.org / jalview.git / blobdiff