JAL-3725 restrict mapped virtual feature location to mapped region

[jalview.git] / src / jalview / io / SequenceAnnotationReport.java

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8e4e783..9ffdf21 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
@@ -207,12 +209,27 @@ public class SequenceAnnotationReport
      * if this is a virtual features, convert begin/end to the
      * coordinates of the sequence it is mapped to
      */
-    int[] beginRange = null;
-    int[] endRange = null;
+    int[] beginRange = null; // feature start in local coordinates
+    int[] endRange = null; // feature end in local coordinates
     if (mf != null)
     {
-      beginRange = mf.getMappedPositions(begin, begin);
-      endRange = mf.getMappedPositions(end, end);
+      if (feature.isContactFeature())
+      {
+        /*
+         * map start and end points individually
+         */
+        beginRange = mf.getMappedPositions(begin, begin);
+        endRange = begin == end ? beginRange
+                : mf.getMappedPositions(end, end);
+      }
+      else
+      {
+        /*
+         * map the feature extent
+         */
+        beginRange = mf.getMappedPositions(begin, end);
+        endRange = beginRange;
+      }
       if (beginRange == null || endRange == null)
       {
         // something went wrong
@@ -273,7 +290,7 @@ public class SequenceAnnotationReport
          * truncate overlong descriptions unless they contain an href
          * before the truncation point (as truncation could leave corrupted html)
          */
-        int linkindex = description.toLowerCase().indexOf("<a ");
+        int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
         boolean hasLink = linkindex > -1
                 && linkindex < MAX_DESCRIPTION_LENGTH;
         if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
@@ -400,8 +417,8 @@ public class SequenceAnnotationReport
                       + "\" target=\""
                       + urllink.get(0)
                       + "\">"
-                      + (urllink.get(0).toLowerCase()
-                              .equals(urllink.get(1).toLowerCase()) ? urllink
+                      + (urllink.get(0).toLowerCase(Locale.ROOT)
+                              .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
                               .get(0) : (urllink.get(0) + ":" + urllink
                                               .get(1)))
                       + "</a><br/>");