X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f498b94abbd5eb688cad365c98a7af9c52eda96;hb=HEAD;hp=7a539d0db1d8f3c4f72d154c756b51999c6c5607;hpb=ceeba9a56384d551389260f71366fe414be37e34;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 7a539d0..1f498b9 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -102,8 +102,8 @@ public class SequenceFeature implements FeatureLocationI
    */
   public SequenceFeature(SequenceFeature cpy)
   {
-    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
-            .getScore());
+    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(),
+            cpy.getScore());
   }
 
   /**
@@ -377,10 +377,10 @@ public class SequenceFeature implements FeatureLocationI
 
   /**
    * Answers the value of the specified attribute as string, or null if no such
-   * value. If more than one attribute name is provided, tries to resolve as keys
-   * to nested maps. For example, if attribute "CSQ" holds a map of key-value
-   * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
-   * in that map.
+   * value. If more than one attribute name is provided, tries to resolve as
+   * keys to nested maps. For example, if attribute "CSQ" holds a map of
+   * key-value pairs, then getValueAsString("CSQ", "Allele") returns the value
+   * of "Allele" in that map.
    * 
    * @param key
    * @return
@@ -605,22 +605,21 @@ public class SequenceFeature implements FeatureLocationI
     sb.append("<br>");
     sb.append("<table>");
     String name = mf == null ? seqName : mf.getLinkedSequenceName();
-    sb.append(String.format(ROW_DATA, "Location", name,
-            begin == end ? begin
-                    : begin + (isContactFeature() ? ":" : "-") + end));
+    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), "<i>imputed by Jalview</i>"));
+        consequence = mf.findProteinVariants(this);
       }
     }
     sb.append(String.format(ROW_DATA, "Type", type, ""));
@@ -635,6 +634,12 @@ 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<>(
@@ -658,8 +663,8 @@ public class SequenceFeature implements FeatureLocationI
           sm.putAll(values);
           for (Entry<?, ?> e : sm.entrySet())
           {
-            sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
-                    .getValue().toString()));
+            sb.append(String.format(ROW_DATA, key, e.getKey().toString(),
+                    e.getValue().toString()));
           }
         }
         else
@@ -673,8 +678,8 @@ public class SequenceFeature implements FeatureLocationI
           String s = entry.getValue().toString();
           if (isValueInteresting(key, s, metadata))
           {
-            sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
-                    : attDesc, s));
+            sb.append(String.format(ROW_DATA, key,
+                    attDesc == null ? "" : attDesc, s));
           }
         }
       }
@@ -712,9 +717,8 @@ public class SequenceFeature implements FeatureLocationI
     }
 
     FeatureAttributeType attType = metadata.getAttributeType(key);
-    if (attType != null
-            && (attType == FeatureAttributeType.Float || attType
-                    .equals(FeatureAttributeType.Integer)))
+    if (attType != null && (attType == FeatureAttributeType.Float
+            || attType.equals(FeatureAttributeType.Integer)))
     {
       try
       {