/*
* append variant in standard format if present
* e.g. p.Arg59Lys
+ * multiple variants are split over lines using <br>
*/
+ boolean asHtml = false;
if (orig != null && !orig.isEmpty() && variants != null
&& !variants.isEmpty())
{
int p = 0;
for (String var : variants)
{
- // TODO proper HGVC nomenclature for delins structural variations
+ // TODO proper HGVS nomenclature for delins structural variations
+ // http://varnomen.hgvs.org/recommendations/protein/variant/delins/
+ // for now we are pragmatic - any orig/variant sequence longer than
+ // three characters is shown with single-character notation rather than
+ // three-letter notation
sb.append("p.");
- for (int c = 0, clen = orig.length(); c < clen; c++)
+ if (orig.length() < 4)
{
- char origchar = orig.charAt(c);
- String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
- sb.append(orig3 == null ? origchar
- : StringUtils.toSentenceCase(orig3));
+ for (int c = 0, clen = orig.length(); c < clen; c++)
+ {
+ char origchar = orig.charAt(c);
+ String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
+ sb.append(orig3 == null ? origchar
+ : StringUtils.toSentenceCase(orig3));
+ }
+ }
+ else
+ {
+ sb.append(orig);
}
sb.append(Integer.toString(uf.getPosition()));
- for (int c = 0, clen = var.length(); c < clen; c++)
+ if (var.length() < 4)
{
- char varchar = var.charAt(c);
- String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
-
- sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
- : "" + varchar);
+ for (int c = 0, clen = var.length(); c < clen; c++)
+ {
+ char varchar = var.charAt(c);
+ String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
+
+ sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
+ : "" + varchar);
+ }
+ }
+ else
+ {
+ sb.append(var);
}
if (++p != variants.size())
{
- sb.append("\n");
+ sb.append("<br/> ");
+ asHtml = true;
}
else
{
{
sb.append(description);
}
+ if (asHtml)
+ {
+ sb.insert(0, "<html>");
+ sb.append("</html>");
+ }
return sb.toString();
}