X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f498b94abbd5eb688cad365c98a7af9c52eda96;hb=HEAD;hp=2dd9cf0d44442e12b3822fed20e61ee1b10f65fe;hpb=3b3c59cfa50e942d2fa5b367b7117cade9459ce7;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2dd9cf0..1f498b9 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
@@ -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("
");
sb.append("