Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2dd9cf0..1f498b9 100755 (executable)
--- 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
@@ -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
@@ -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 +604,24 @@ public class SequenceFeature implements FeatureLocationI
     StringBuilder sb = new StringBuilder(128);
     sb.append("<br>");
     sb.append("<table>");
-    sb.append(String.format(ROW_DATA, "Location", seqName,
-            begin == end ? begin
-                    : begin + (isContactFeature() ? ":" : "-") + end));
+    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[] 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())
+      {
+        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 +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<>(
@@ -638,8 +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
@@ -653,8 +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));
           }
         }
       }
@@ -692,9 +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
       {