*/
package jalview.datamodel;
-import jalview.datamodel.features.FeatureAttributeType;
-import jalview.datamodel.features.FeatureAttributes;
-import jalview.datamodel.features.FeatureLocationI;
-import jalview.datamodel.features.FeatureSourceI;
-import jalview.datamodel.features.FeatureSources;
-import jalview.util.StringUtils;
-
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.TreeMap;
import java.util.Vector;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureAttributes;
+import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
+import jalview.util.StringUtils;
+
/**
* A class that models a single contiguous feature on a sequence. If flag
* 'contactFeature' is true, the start and end positions are interpreted instead
}
/**
- * Answers an html-formatted report of feature details
+ * Answers an html-formatted report of feature details. If parameter
+ * {@code mf} is not null, the feature is a virtual linked feature, and
+ * details included both the original location and the mapped location
+ * (CDS/peptide).
*
* @param seqName
+ * @param mf
*
* @return
*/
- public String getDetailsReport(String seqName)
+ public String getDetailsReport(String seqName, MappedFeatures mf)
{
FeatureSourceI metadata = FeatureSources.getInstance()
.getSource(source);
StringBuilder sb = new StringBuilder(128);
sb.append("<br>");
sb.append("<table>");
- sb.append(String.format(ROW_DATA, "Location", seqName,
+ String name = mf == null ? seqName : mf.getLinkedSequenceName();
+ sb.append(String.format(ROW_DATA, "Location", name,
begin == end ? begin
: begin + (isContactFeature() ? ":" : "-") + end));
+
+ String consequence = "";
+ if (mf != null)
+ {
+ int[] beginRange = mf.getMappedPositions(begin, begin);
+ int[] endRange = mf.getMappedPositions(end, end);
+ int from = beginRange[0];
+ int to = endRange[endRange.length - 1];
+ String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
+ sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
+ : from + (isContactFeature() ? ":" : "-") + to));
+ if (mf.isFromCds())
+ {
+ consequence = mf.findProteinVariants(this);
+ }
+ }
sb.append(String.format(ROW_DATA, "Type", type, ""));
String desc = StringUtils.stripHtmlTags(description);
sb.append(String.format(ROW_DATA, "Description", desc, ""));
sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
}
+ if (!consequence.isEmpty())
+ {
+ sb.append(String.format(ROW_DATA, "Consequence",
+ "<i>Translated by Jalview</i>", consequence));
+ }
+
if (otherDetails != null)
{
TreeMap<String, Object> ordered = new TreeMap<>(