X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FDnaUtils.java;fp=src%2Fjalview%2Futil%2FDnaUtils.java;h=9582e2ea1938c7bfcac3d25844573a8a986c542d;hb=f2b03e9fecf41886ebf5f747fd4be02edf042bee;hp=0000000000000000000000000000000000000000;hpb=d737688dfdb8d00ed63a699fb86548499d75bcf2;p=jalview.git
diff --git a/src/jalview/util/DnaUtils.java b/src/jalview/util/DnaUtils.java
new file mode 100644
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--- /dev/null
+++ b/src/jalview/util/DnaUtils.java
@@ -0,0 +1,133 @@
+package jalview.util;
+
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class DnaUtils
+{
+
+ /**
+ * Parses an ENA/GenBank format location specifier and returns a list of
+ * [start, end] ranges. Throws an exception if not able to parse.
+ *
+ * Currently we do not parse "order()" specifiers, or indeterminate ranges of
+ * the format "<start..end" or "start..>end" or "start.end" or
+ * "start^end"
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ * if unable to parse the location (the exception message is the
+ * location specifier being parsed); we use ParseException in
+ * preference to the unchecked IllegalArgumentException
+ * @see http://www.insdc.org/files/feature_table.html#3.4
+ */
+ public static List parseLocation(String location)
+ throws ParseException
+ {
+ if (location.startsWith("join("))
+ {
+ return parseJoin(location);
+ }
+ else if (location.startsWith("complement("))
+ {
+ return parseComplement(location);
+ }
+ if (location.startsWith("order("))
+ {
+ throw new ParseException(location, 0);
+ }
+
+ /*
+ * try to parse m..n (or simply m)
+ */
+ 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]);
+ return Collections.singletonList(new int[] { start, end });
+ } catch (NumberFormatException e)
+ {
+ /*
+ * could be a location like <1..888 or 1..>888
+ */
+ throw new ParseException(location, 0);
+ }
+ }
+ else
+ {
+ /*
+ * could be a location like 102.110 or 123^124
+ */
+ throw new ParseException(location, 0);
+ }
+ }
+
+ /**
+ * Parses a complement(locationSpec) into a list of start-end ranges
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ */
+ static List parseComplement(String location) throws ParseException
+ {
+ /*
+ * take what is inside complement()
+ */
+ if (!location.endsWith(")"))
+ {
+ throw new ParseException(location, 0);
+ }
+ String toComplement = location.substring("complement(".length(),
+ location.length() - 1);
+ List ranges = parseLocation(toComplement);
+
+ /*
+ * reverse the order and direction of ranges
+ */
+ Collections.reverse(ranges);
+ for (int[] range : ranges)
+ {
+ int temp = range[0];
+ range[0] = range[1];
+ range[1] = temp;
+ }
+ return ranges;
+ }
+
+ /**
+ * Parses a join(loc1,loc2,...,locn) into a list of start-end ranges
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ */
+ static List parseJoin(String location) throws ParseException
+ {
+ List ranges = new ArrayList();
+
+ /*
+ * take what is inside join()
+ */
+ if (!location.endsWith(")"))
+ {
+ throw new ParseException(location, 0);
+ }
+ String joinedLocs = location.substring("join(".length(),
+ location.length() - 1);
+ String[] locations = joinedLocs.split(",");
+ for (String loc : locations)
+ {
+ List range = parseLocation(loc);
+ ranges.addAll(range);
+ }
+ return ranges;
+ }
+
+}