JAL-2114 accept "<123..178" or "123..>178" format

[jalview.git] / src / jalview / util / DnaUtils.java

diff --git a/src/jalview/util/DnaUtils.java b/src/jalview/util/DnaUtils.java
index 9ab4fda..f6514e5 100644 (file)
--- a/src/jalview/util/DnaUtils.java
+++ b/src/jalview/util/DnaUtils.java
@@ -35,14 +35,15 @@ public class DnaUtils
 
     /*
      * try to parse m..n (or simply m)
+     * also handles <m..n or m..>n (discarding < or >)
      */
     String[] range = location.split("\\.\\.");
     if (range.length == 1 || range.length == 2)
     {
       try
       {
-        int start = Integer.valueOf(range[0]);
-        int end = range.length == 1 ? start : Integer.valueOf(range[1]);
+        int start = parseRangeEnd(range[0]);
+        int end = range.length == 1 ? start : parseRangeEnd(range[1]);
         return Collections.singletonList(new int[] { start, end });
       } catch (NumberFormatException e)
       {
@@ -64,6 +65,22 @@ public class DnaUtils
   }
 
   /**
+   * Returns the integer value of a locus, discarding any < or > prefix
+   * 
+   * @throws NumberFormatException
+   *           if value is not numeric
+   */
+  static int parseRangeEnd(String loc)
+  {
+
+    if (loc.startsWith("<") || loc.startsWith(">"))
+    {
+      loc = loc.substring(1);
+    }
+    return Integer.valueOf(loc);
+  }
+
+  /**
    * Parses a complement(locationSpec) into a list of start-end ranges
    * 
    * @param location