X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=6eeba2fbbb60119c53a7f2bfca4b464fe5076ee1;hb=refs%2Fheads%2Fpatch%2FJAL-3561_JAL-3660_fileformatexport_CLI;hp=2dd9cf0d44442e12b3822fed20e61ee1b10f65fe;hpb=3b3c59cfa50e942d2fa5b367b7117cade9459ce7;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2dd9cf0..6eeba2f 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,13 +20,6 @@
  */
 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;
@@ -35,6 +28,13 @@ import java.util.SortedMap;
 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
@@ -586,13 +586,17 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
-   * 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);
@@ -600,9 +604,26 @@ public class SequenceFeature implements FeatureLocationI
     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, ""));
@@ -615,6 +636,12 @@ public class SequenceFeature implements FeatureLocationI
       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<>(