import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
*/
public class SequenceAnnotationReport
{
+ private static final int MAX_DESCRIPTION_LENGTH = 40;
+
private static final String COMMA = ",";
private static final String ELLIPSIS = "...";
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
- if (ref1.isChromosome())
+ if (ref1 instanceof GeneLociI)
{
return -1;
}
- if (ref2.isChromosome())
+ if (ref2 instanceof GeneLociI)
{
return 1;
}
}
/**
- * Append text for the list of features to the tooltip
+ * Append text for the list of features to the tooltip Returns number of
+ * features left if maxlength limit is (or would have been) reached
*
* @param sb
- * @param rpos
+ * @param residuePos
* @param features
* @param minmax
+ * @param maxlength
*/
- public void appendFeatures(final StringBuilder sb, int rpos,
+ public int appendFeaturesLengthLimit(final StringBuilder sb,
+ int residuePos, List<SequenceFeature> features,
+ FeatureRendererModel fr, int maxlength)
+ {
+ for (int i = 0; i < features.size(); i++)
+ {
+ SequenceFeature feature = features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+ {
+ return features.size() - i;
+ }
+ }
+ return 0;
+ }
+
+ public void appendFeatures(final StringBuilder sb, int residuePos,
List<SequenceFeature> features, FeatureRendererModel fr)
{
- if (features != null)
+ appendFeaturesLengthLimit(sb, residuePos, features, fr, 0);
+ }
+
+ /**
+ * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
+ * Returns number of features left if maxlength limit is (or would have been)
+ * reached
+ *
+ * @param sb
+ * @param residuePos
+ * @param mf
+ * @param fr
+ * @param maxlength
+ */
+ public int appendFeaturesLengthLimit(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr, int maxlength)
+ {
+ for (int i = 0; i < mf.features.size(); i++)
{
- for (SequenceFeature feature : features)
+ SequenceFeature feature = mf.features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
{
- appendFeature(sb, rpos, fr, feature);
+ return mf.features.size() - i;
}
}
+ return 0;
+ }
+
+ public void appendFeatures(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr)
+ {
+ appendFeaturesLengthLimit(sb, residuePos, mf, fr, 0);
}
/**
* @param minmax
* @param feature
*/
- void appendFeature(final StringBuilder sb, int rpos,
- FeatureRendererModel fr, SequenceFeature feature)
+ boolean appendFeature(final StringBuilder sb0, int rpos,
+ FeatureRendererModel fr, SequenceFeature feature,
+ MappedFeatures mf, int maxlength)
{
+ StringBuilder sb = new StringBuilder();
if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
- if (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
sb.append(feature.getType()).append(" ").append(feature.getBegin())
.append(":").append(feature.getEnd());
}
- return;
+ return appendTextMaxLengthReached(sb0, sb, maxlength);
}
- if (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
// TODO: remove this hack to display link only features
boolean linkOnly = feature.getValue("linkonly") != null;
if (description != null && !description.equals(feature.getType()))
{
description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * truncate overlong descriptions unless they contain an href
+ * before the truncation point (as truncation could leave corrupted html)
+ */
+ int linkindex = description.toLowerCase().indexOf("<a ");
+ boolean hasLink = linkindex > -1
+ && linkindex < MAX_DESCRIPTION_LENGTH;
+ if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ {
+ description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ + ELLIPSIS;
+ }
+
sb.append("; ").append(description);
}
}
}
}
+
+ if (mf != null)
+ {
+ String variants = mf.findProteinVariants(feature);
+ if (!variants.isEmpty())
+ {
+ sb.append(" ").append(variants);
+ }
+ }
+ }
+ return appendTextMaxLengthReached(sb0, sb, maxlength);
+ }
+
+ void appendFeature(final StringBuilder sb, int rpos,
+ FeatureRendererModel fr, SequenceFeature feature,
+ MappedFeatures mf)
+ {
+ appendFeature(sb, rpos, fr, feature, mf, 0);
+ }
+
+ private static boolean appendTextMaxLengthReached(StringBuilder sb0,
+ StringBuilder sb, int maxlength)
+ {
+ boolean ret = false;
+ if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
+ {
+ sb0.append(sb);
+ return false;
+ } else {
+ return true;
}
}
+ (urllink.get(0).toLowerCase()
.equals(urllink.get(1).toLowerCase()) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
- .get(1))) + "</a></br>");
+ .get(1)))
+ + "</a><br/>");
}
} catch (Exception x)
{
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("<br>").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
SequenceI ds = sequence;
.getNonPositionalFeatures())
{
int sz = -sb.length();
- appendFeature(sb, 0, fr, sf);
+ appendFeature(sb, 0, fr, sf, null);
sz += sb.length();
maxWidth = Math.max(maxWidth, sz);
}
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
}
if (moreSources)
{
- sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
+ sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("<br>(");
+ sb.append("<br/>(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}
git://source.jalview.org / jalview.git / blobdiff