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>()
{
void appendFeature(final StringBuilder sb, int rpos,
Map<String, float[][]> minmax, SequenceFeature feature)
{
- String tmpString;
- if (feature.getType().equals("disulfide bond"))
+ if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
{
sb.append("<br>");
}
- sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+ sb.append(feature.getType()).append(" ").append(feature.getBegin())
+ .append(":")
.append(feature.getEnd());
}
}
if (feature.getDescription() != null
&& !feature.description.equals(feature.getType()))
{
- tmpString = feature.getDescription();
+ String tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : ((float[][]) 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=" + feature.getScore());
+ sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
}
String status = (String) feature.getValue("status");
{
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,