X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=bbf1b4515595fdc5837e1384a47cb046259237e1;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=df268f8dc711f8984d55c966ce8a4368ff759cca;hpb=5a631296dd1dcc1df7b50487a647c27333696c74;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index df268f8..bbf1b45 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -608,19 +608,19 @@ public class SequenceFeature implements FeatureLocationI
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];
+ int[] localRange = mf.getMappedPositions(begin, end);
+ int from = localRange[0];
+ int to = localRange[localRange.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())
{
- sb.append(String.format(ROW_DATA, "Consequence",
- mf.findProteinVariants(this), ""));
+ consequence = mf.findProteinVariants(this);
}
}
sb.append(String.format(ROW_DATA, "Type", type, ""));
@@ -635,6 +635,12 @@ public class SequenceFeature implements FeatureLocationI
sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
}
+ if (!consequence.isEmpty())
+ {
+ sb.append(String.format(ROW_DATA, "Consequence",
+ "Translated by Jalview", consequence));
+ }
+
if (otherDetails != null)
{
TreeMap ordered = new TreeMap<>(