X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Futil%2FDnaUtils.java;h=284ec107f818b5b039ef993f615041b2a95f35e1;hb=refs%2Fheads%2FRelease_2_9_Branch;hp=9ab4fdab248f7a7a671dceffd04571b4aec2c276;hpb=ede02500a0240fd0e2c6780ff5ab8e1d254a9a26;p=jalview.git
diff --git a/src/jalview/util/DnaUtils.java b/src/jalview/util/DnaUtils.java
index 9ab4fda..284ec10 100644
--- a/src/jalview/util/DnaUtils.java
+++ b/src/jalview/util/DnaUtils.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.util;
+import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
@@ -9,13 +30,22 @@ public class DnaUtils
/**
* Parses an ENA/GenBank format location specifier and returns a list of
- * [start, end] ranges. Returns null if not able to parse.
+ * [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("))
{
@@ -25,12 +55,9 @@ public class DnaUtils
{
return parseComplement(location);
}
- String errorMessage = "Unable to process location specifier: "
- + location;
if (location.startsWith("order("))
{
- System.err.println(errorMessage);
- return null;
+ throw new ParseException(location, 0);
}
/*
@@ -49,8 +76,7 @@ public class DnaUtils
/*
* could be a location like <1..888 or 1..>888
*/
- System.err.println(errorMessage);
- return null;
+ throw new ParseException(location, 0);
}
}
else
@@ -58,8 +84,7 @@ public class DnaUtils
/*
* could be a location like 102.110 or 123^124
*/
- System.err.println(errorMessage);
- return null;
+ throw new ParseException(location, 0);
}
}
@@ -68,26 +93,20 @@ public class DnaUtils
*
* @param location
* @return
+ * @throws ParseException
*/
- static List parseComplement(String location)
+ static List parseComplement(String location) throws ParseException
{
/*
* take what is inside complement()
*/
if (!location.endsWith(")"))
{
- return null;
+ throw new ParseException(location, 0);
}
String toComplement = location.substring("complement(".length(),
location.length() - 1);
List ranges = parseLocation(toComplement);
- if (ranges == null)
- {
- /*
- * something bad in there
- */
- return null;
- }
/*
* reverse the order and direction of ranges
@@ -107,8 +126,9 @@ public class DnaUtils
*
* @param location
* @return
+ * @throws ParseException
*/
- static List parseJoin(String location)
+ static List parseJoin(String location) throws ParseException
{
List ranges = new ArrayList();
@@ -117,7 +137,7 @@ public class DnaUtils
*/
if (!location.endsWith(")"))
{
- return null;
+ throw new ParseException(location, 0);
}
String joinedLocs = location.substring("join(".length(),
location.length() - 1);
@@ -125,17 +145,7 @@ public class DnaUtils
for (String loc : locations)
{
List range = parseLocation(loc);
- if (range == null)
- {
- /*
- * something bad in there
- */
- return null;
- }
- else
- {
- ranges.addAll(range);
- }
+ ranges.addAll(range);
}
return ranges;
}